Did the prophet's companions ever refuse to do what he asked of them?

In a Nutshell: Yes, this sometimes occurred. Where it was limited to matters of choice the prophet (saw) let them be; where it was not he would chide them. Common examples include the writing of the treaty of Hudaybiyyah where the pilgrimage could not be completed and the archers moving from their positions in the battle of Uhud or individual companions like Imam Ali not removing the prophet's name from a treaty and the suggestions presented by companions such as al-Hubab and Salman (ra). Background The Companions (ra) used to obey the Prophet (saw) in any situation, whether his decision was based on revelation, approved by the revelation or his mere personal opinion. The companions used to obey the Prophet (saw) in all situations because the Qur'an contains many verses prescribing obedience to the Prophet's orders and prohibitions and warn against disobedience. For example, Allah says:  فَلْيَحْذَرِ الَّذِينَ يُخَالِفُونَ عَنْ أَمْرِهِ أَنْ تُصِيبَهُمْ فِتْنَةٌ أَوْ يُصِيبَهُمْ عَذَابٌ أَلِيمٌ "So let those beware who dissent from the Prophet's order, lest fitnah strikes them or a painful punishment." (Qur'an 24:63)  They would even obey him in worldly life affairs such as the situation of cross-pollination of date palm trees where he made a personal remark.  But there are some individual cases where a group of the companions (ra) collectively refused to perform what the Prophet (saw) ordered them to do, or an individual companion refused to do due to their ijtihad, misunderstanding or mistake. Some of them were blamed for their disobedience, others were not.  Al-Hudaybiyyah Treaty For example, in the treaty of al-Hudaybiyah, the Prophet (saw) Ali ibn Abi Talib (ra) was the scribe responsible for drafting the treaty. When the other party rejected labelling the Prophet (saw) with the Messenger of Allah, the Prophet (saw) agreed to pass the treaty. But when he asked Ali (ra) to erase the word Messenger of Allah, Ali (ra) refused out of his love and loyalty to the Prophet (saw) so the Prophet (saw) did it himself.  Bukhari narrated: فَقَالَ لِعَلِيٍّ ‏"‏ امْحُ رَسُولَ اللَّهِ ‏"‏‏.‏ فَقَالَ عَلِيٌّ وَاللَّهِ لاَ أَمْحَاهُ أَبَدًا‏.‏ قَالَ ‏"‏ فَأَرِنِيهِ ‏"‏‏.‏ قَالَ فَأَرَاهُ إِيَّاهُ، فَمَحَاهُ النَّبِيُّ صلى الله عليه وسلم بِيَدِهِ  "He (the Prophet) asked Ali to erase the expression of Apostle of Allah. On that Ali said, 'By Allah, I will never erase it.' Allah's Apostle said (to Ali), 'Let me see the phrase. When Ali showed him the phrase, the Prophet (saw) erased the expression with his own hand." (Sahih al-Bukhari 3184) The Prophet (saw) did not blame Ali (ra) because of his pure intention and confession of the Prophethood of Muhammad (saw).  Umar was also upset with the terms of the treaty and tried to cancel the establishment of the treaty by several means; for example, he went to the Prophet (saw) and Abu Bakr (ra) and objected; he asked the son of the envoy of Quraysh to kill his father; he thought of having a group of the companions and attack Mecca.  Umar Ibn Khattab (ra) exemplifies this well with his confusion and surprise. He narrates: فَقَالَ عُمَرُ بْنُ الْخَطَّابِ : وَاللَّهِ مَا شَكَكْتُ مُنْذُ أَسْلَمْتُ إِلَّا يَوْمَئِذٍ  قَالَ : فَأَتَيْتُ النَّبِيَّ صَلَّى اللَّهُ عَلَيْهِ وَسَلَّمَ ، فَقُلْتُ : أَلَسْتَ نَبِيَّ اللَّهِ حَقًّا ؟  قَالَ : بَلَى قَالَ : قُلْتُ أَلَسْنَا عَلَى الْحَقِّ ؟ وَعَدُوُّنَا عَلَى الْبَاطِلِ ؟  قَالَ : بَلَى قُلْتُ : فَلِمَ نُعْطَى الدَّنِيَّةَ فِي دِينِنَا ؟ فَقَالَ : إِنِّي رَسُولُ اللَّهِ وَلَسْتُ أَعْصِيهِ ، وَهُوَ نَاصِرِي   قُلْتُ : أَوَ لَسْتَ كُنْتَ تُحَدِّثُنَا أَنَّا سَنَأْتِي الْبَيْتَ فَنَطُوفُ بِهِ ؟ قَالَ : بَلَى ، فَأَخْبَرْتُكَ أَنَّكَ تَأْتِيهِ الْعَامَ قُلْتُ : لَا   قَالَ : فَإِنَّكَ آتِيهِ وَمُطَوِّفٌ بِهِ  "I never doubted my Islam except on that day."   I came to the Prophet (saw) and asked, "Are you not truly the Messenger of Allah (saw)?"  The Prophet (saw) said, "Yes, indeed."  I asked, "Is not our cause just and the cause of the enemy unjust?"  The Prophet (saw) said, "Yes."  I asked, "Then why should we be humiliated in our religion?"  He (saw) said, "I am Allah's Messenger; I do not disobey Him and He will make me victorious."  I asked, "Did you not tell us that we would go to the Ka'bah and perform Tawaf around it?"  He (saw) said, "Yes, but did I tell you that we would visit the Ka'bah this year?"  I replied, "No."  He (saw) said, "So you will visit it and perform Tawaf around it!" (Musanaf Abd al-Razaq Hdith 9419) So the Prophet (saw) corrected Umar's understanding of the event and Umar himself knew he was wrong and made kafarat (atonement) for the sin. The rest of the companions collectively refused the Prophet's (saw) order to shave their heads and slaughter their sacrifice.  The Qur'an acknowledged this, their love for the victory of Islam, with what appeared to be a defeat by this treaty and its unfair terms the Prophet (saw) approved. Allah, in Surat al-Fath (the victory), explains the reason for the treaty and how it was to be a great victory to Muslims.  فَأَنزَلَ اللَّهُ سَكِينَتَهُ عَلَىٰ رَسُولِهِ وَعَلَى الْمُؤْمِنِينَ وَأَلْزَمَهُمْ كَلِمَةَ التَّقْوَىٰ وَكَانُوا أَحَقَّ بِهَا وَأَهْلَهَا ۚ وَكَانَ اللَّهُ بِكُلِّ شَيْءٍ عَلِيمًا ... مُّحَمَّدٌ رَّسُولُ اللَّهِ ۚ وَالَّذِينَ مَعَهُ أَشِدَّاءُ عَلَى الْكُفَّارِ رُحَمَاءُ بَيْنَهُمْ ۖ تَرَاهُمْ رُكَّعًا سُجَّدًا يَبْتَغُونَ فَضْلًا مِّنَ اللَّهِ وَرِضْوَانًا "But Allah sent down His tranquillity upon His Messenger and upon the believers and imposed upon them the word of righteousness, and they were more deserving of it and worthy of it. And ever is Allah, of all things, Knowing. Muhammad is the Messenger of Allah; and those with him are forceful against the disbelievers, merciful among themselves. You see them bowing and prostrating (in prayer), seeking bounty from Allah and (His) pleasure." (Qur'an 48:26-29) Allah then promised them they would soon enter Mecca without fear, the greatest victory.   لَّقَدْ صَدَقَ اللَّهُ رَسُولَهُ الرُّؤْيَا بِالْحَقِّ ۖ لَتَدْخُلُنَّ الْمَسْجِدَ الْحَرَامَ إِن شَاءَ اللَّهُ آمِنِينَ مُحَلِّقِينَ رُءُوسَكُمْ وَمُقَصِّرِينَ لَا تَخَافُونَ ۖ فَعَلِمَ مَا لَمْ تَعْلَمُوا فَجَعَلَ مِن دُونِ ذَٰلِكَ فَتْحًا قَرِيبًا هُوَ الَّذِي أَرْسَلَ رَسُولَهُ بِالْهُدَىٰ وَدِينِ الْحَقِّ لِيُظْهِرَهُ عَلَى الدِّينِ كُلِّهِ ۚ وَكَفَىٰ بِاللَّهِ شَهِيدًا "Certainly has Allah showed to His Messenger the vision in truth. You will surely enter al-Masjid al-Haram, if Allah wills, in safety, with your heads shaved and (hair) shortened, not fearing (anyone). He knew what you did not know and has arranged before that a conquest near (at hand). It is He who sent His Messenger with guidance and the religion of truth to manifest it over all religion. And sufficient is Allah as Witness." (Qur'an 48:27-28) The Battle of Badr Before the initiation of the battle of Badr, during its preparation, the Prophet (saw) decided to rest the army in a certain place waiting for the coming of Quraysh's army. The companion Al-Hubab ibn al-Mundhir (ra) saw this location was not strategically sensible for the Muslim army; so he went to the Prophet (saw) and asked him whether this decision was based on revelation or on a personal opinion. The Prophet (saw) told him it was his plan and was not revelation. Al-Habab (ra) then offered a better plan which the Prophet (saw) approved and thanked him for his contribution. The early historian Ibn Hisham narrated: أَنَّ الْحُبَابَ بْنَ الْمُنْذِرِ بْنِ الْجَمُوحِ قَالَ: يَا رَسُولَ اللَّهِ، أَرَأَيْتَ هَذَا الْمَنْزِلَ، أَمَنْزِلًا أَنْزَلَكَهُ اللَّهُ لَيْسَ لَنَا أَنْ نَتَقَدَّمَهُ، وَلَا نَتَأَخَّرَ عَنْهُ، أَمْ هُوَ الرَّأْيُ وَالْحَرْبُ وَالْمَكِيدَةُ؟ قَالَ: بَلْ هُوَ الرَّأْيُ وَالْحَرْبُ وَالْمَكِيدَةُ؟ فَقَالَ: يَا رَسُولَ اللَّهِ، فَإِنَّ هَذَا لَيْسَ بِمَنْزِلِ، فَانْهَضْ بِالنَّاسِ حَتَّى نَأْتِيَ أَدْنَى مَاءٍ مِنْ الْقَوْمِ، فَنَنْزِلَهُ، ثُمَّ نُغَوِّرُ مَا وَرَاءَهُ مِنْ الْقُلُبِ، ثُمَّ نَبْنِي عَلَيْهِ حَوْضًا فَنَمْلَؤُهُ مَاءً، ثُمَّ نُقَاتِلُ الْقَوْمَ، فَنَشْرَبُ وَلَا يَشْرَبُونَ، فَقَالَ رَسُولُ اللَّهِ صَلَّى اللهُ عَلَيْهِ وَسَلَّمَ: لَقَدْ أَشَرْتَ بِالرَّأْيِ. "Al-Hubab ibn al-Mundhir ibn al-Jamuh said: 'O the Messanger of Allah, is your plan to stay here is appointed by Allah that we don't have to change or is it a (personal) opinion for war planning and tricks?' The Prophet (saw) answered, 'No, it is a (personal) opinion for war planning and tricks.' Al-Hubab said, 'okay, this is not a good place for the army. So I suggest taking the army to the closest source of water to our enemy and stay there, then destroy any other well and build a basin and fill it with water. Consequently, we will drink but our enemy won't.' The Prophet (saw) said, 'you have suggested the right decision.' and fulfilled it." (Ibn Hisham, as-Seera al-Nabawiyah, Vol. 1, p. 620) The same situation was repeated with the suggestion of the Persian Companion Salman who suggested adopting the Persian tactic of digging a trench to protect the entrance to Medina. The Battle of Uhud In the Battle of Uhud, the Prophet (saw) chose a strategic place for his army and appointed a group of archers to cover their rear. The Prophet (saw) ordered them not to leave their positions, whether in victory or defeat. At the start of the battle, Muslims appeared to win and the enemies fled leaving behind huge spoils; the archers promptly left their places seeking spoils, a decision that cost them defeat in the battle as Quraysh promptly attacked from the rear. The Qur'an criticised their disobedience to the Prophet (saw):  وَلَقَدْ صَدَقَكُمُ اللَّهُ وَعْدَهُ إِذْ تَحُسُّونَهُم بِإِذْنِهِ ۖ حَتَّىٰ إِذَا فَشِلْتُمْ وَتَنَازَعْتُمْ فِي الْأَمْرِ وَعَصَيْتُم مِّن بَعْدِ مَا أَرَاكُم مَّا تُحِبُّونَ ۚ مِنكُم مَّن يُرِيدُ الدُّنْيَا وَمِنكُم مَّن يُرِيدُ الْآخِرَةَ ۚ ثُمَّ صَرَفَكُمْ عَنْهُمْ لِيَبْتَلِيَكُمْ ۖ وَلَقَدْ عَفَا عَنكُمْ ۗ وَاللَّهُ ذُو فَضْلٍ عَلَى الْمُؤْمِنِينَ "And Allah had certainly fulfilled His promise to you (for believers victory that you found it) when you were killing the enemy by His permission until (the time) when you lost courage and fell to disputing about the order (given by the Prophet) and disobeyed after He had shown you that which you love (spoil). Among you (the archers) are some who desire this world, and among you are some who desire the Hereafter. Then he turned you back from them [defeated] that He might test you. And He has already forgiven you, and Allah is the possessor of bounty for the believers." (Qur'an 3:152) Even in this situation, Allah forgave their sin as they repented and they were sincerely not wanting to harm or cause defeat.   Conclusion The Companions (ra) used to obey the Prophet (saw) in any situation, whether his decision was based on revelation, approved by the revelation or his mere personal opinion. In some situations, the companions had refused to obey the Prophet's order, out of their love for the victory of Islam, based on a misunderstanding of the reason for the Prophet's acts.