THE AFFAIR OF MUHAYYISA AND HUWAYYISA
“The apostle said, ‘kill any Jew that falls into your power.’ Thereupon Muhayyisa b. Mas’ud leapt upon Ibn Sunayna, a Jewish merchant with whom they had social and business relations, and killed him. Huwayyisa was not a Muslim at the time though he was the elder brother.” 
Narrated Muhayyisah: The Apostle of Allah (p) said: If you gain a victory over the men of Jews, kill them. So Muhayyisah jumped over Shubaybah, a man of the Jewish merchants. He had close relations with them. He then killed him. At that time Huwayyisah (brother of Muhayyisah) had not embraced Islam. He was older than Muhayyisah. When he killed him, Huwayyisah beat him and said: O enemy of Allah, I swear by Allah, you have a good deal of fat in your belly from his property. – (Abu Dawud Book 19, Number 2996)
It is alleged from the above that Prophet Mohammad (p) gave an order to his companions that they can kill any Jew with impunity. This cannot be true, since the highest authority, which is the Quran, declares that you should only fight those who fight you first. Muslims are not allowed to take an innocent life.
“Allah does not forbid you from those who do not fight you because of religion and do not expel you from your homes – from being righteous toward them and acting justly toward them. Indeed, Allah loves those who act justly. Allah only forbids you from those who fight you because of religion and expel you from your homes and aid in your expulsion – [forbids] that you make allies of them. And whoever makes allies of them, then it is those who are the wrongdoers.” – Quran 60:8-9
This story goes against the Prophet’s character and even the highest authority, the Quran which Muslims follow. If the Prophet (p) gave such an order, would only one Jew be killed? Therefore, the story is untrue.
Islamic scholar Muhammad Nasiruddin al-Albani declared the story in Abu Dawud as ‘weak’. Meaning, the story being spread around is false.
Furthermore, the following scholars also further elaborate that this story is not true.
THE ALLEGED PERMISSION TO KILL THE JEWS
It is related by some of the biographers of Mohammad, eagerly recited by others of Europe, that, ‘on the morning after the murder of Kab, Mahomet gave a general permission to his followers to slay any Jews whom they might chance to meet,’ and that the murder of Ibn Sanina, a Jewish merchant, by Muheiasa, a Moslem, was the direct consequence of this order. ‘When Huweisa upbraided Muneiasa for killing his confederate the Jew, and appropriating his wealth, – ‘By the Lord!’ replied Muheiasa, ‘if he that commanded me to kill him commanded to kill thee also, I would have done it.’ ‘What!’ Huweisa cried, ‘wouldst thou have slain thine own brother at Mahomet’s bidding?’ – ‘Even so,’ answered the fanatic. ‘Strange indeed!’ Huweisa responded. ‘Hath the new religion reached to this pitch! Verily it is a wonderful Faith.’ And Huweisa was converted from that very hour.’
Ibn Is-hak says this story was related to him by a freedom of the Bani Harisa tribe from the daughter of Muheiasa, who had heard it from her father. (1) Now there is nothing known of this mysterious person, the freedman of the tribe of Haris, therefore no reliance can be put on his story.
(2) We have no knowledge of the daughter of the murdered Muheiasa, or Moheisa, as he called by the biographer, Ibn Hisham.
(3) Muheiasa himself has not that respectable character which can lend even a shadow of veracity to his narration.
(4) And lastly, the story that Mohammad had given general permission to his followers to slay any Jew whom they might chance to meet, and consequently Muheiasa killed Ibn Sanina, and Huweisa became a convert to Islam, is contradicted by other counter-tradition in Ibn Hisham (…), who has related from Abu Obeida, who relates from Abu Omar-al-Madani that, ‘during the execution of the Bani Koreiza (vide para. 68), one Kab-bin-Yahooza was made over to Muheiasa for execution. When the latter executed his victim, Huweisa, his brother, who was still unbelieving, upbraided Muheiasa. ‘If he,’ responded Muheiasa, ‘that commanded me to kill him had commanded me to kill thee also, I would have killed thee.’ Huweisa was quite surprised at his brother’s reply, and went away astonished. During the night he used to wake up repeatedly, and wonder at his brother’s staunch devotion to his faith. In the morning, he said, ‘By the Lord! This is a wonderful faith,’ and came to the Prophet to embrace Islam. These remarks show that the alleged permission to kill the Jews, and Ibn Sanina’s murder, and Huweisa’s conversion in consequence thereof, is all a mere concoction.
Even Sir W. Muir, though very fond of collecting all such apocryphal traditions reflecting on the character of the Prophet, doubts the veracity of this one, and declares its improbability and inexpediency. He writes:-
‘But the order itself is a strange one, and must, one would suppose, have been accompanied by some conditions or reservations not here apparent. It was surely not expedient for the Prophet’s cause at this tme that the streets of Medina should have flowed with blood by the strict execution of this command. Yet such is the distinct tenor of the best traditions.
‘The order was not an unlikely one to have issued at a time when Mahomet was irritated against the Jews by their treachery; and Hishami has a tradition that it was promulgated when Mahomet directed the massacre of all the males of the Coreitza,, which would have been the more likely version if the other tradition had not been so strong and positive.’
But the tradition quoted by him is by no means the best or strongest as I have shown above. Hishamee does not say that the order was promulgated at the execution of the Bani Koreiza. He simply narrates the story of Muheiasa and Huweisa to have taken plave at that time. 
Maulana Muhammad Ali:
Infact, as the Hidayah has put it clearly, a person’s life, unless he is a murdered, cannot be taken in any ground other than that he is a combatant: ‘And they should not kill a woman, nor a child, nor an aged person, nor one who does not take part in a war, nor a blind man, because what makes it lawful to take a man’s life, according to us, is his being a combatant, and this not true in their case’ (Ch. Kaifiyyat al-Qital). In fact, this conclusion, which is the basic principel of the Hanifite law, is based on the express words of the Holy Prophet himself. As Abu Dawud reports on the authority of Rabah, son of Rabi: ‘We were with the Prophet in a certain battle, and he saw the people gather together in one place. So he sent a man to make an inquiry as to why the people had gathered together. The messenger came back and said, ‘there is a woman killed.’ The Holy Prophet said, ‘she was not fighting’. The reported says that Khalid was leading at the time. So the Prophet sent a man to Khalid and asked him to tell Khalid that he should not kill a woman nor a hireling’. (Ch. Qatl al-Nisa).
By remarking that ‘she was not fighting’, the Holy prophet made it plain that even in battle only such persons could be killed as actually took part in fighting, and along with women he excepted hirelings, because they were only hired for other work and did not take part in actual fighting. It is on this basis that the Hanifite law accepts, along with women, children and old men, all such persons as cannot take part in fighting. And the conclusion is inevitable that according to the Holy prophet’s own injunctions the killing of a person was not lawful unless he took part in fighting, and no report to the effect that a person was killed though he was not a combatant is either untrue or defective, even if it is met with a reliable collection of traditions. And as for biographies, they cannot be trusted at all in such matters, and the case of Ibn Sunainah’s murder must be rejected as untrue. The statement that this murder was due to the Prophet giving a general order for the slaughter of the Jews is sufficient to discredit this report, for not only would such an order be against the clear injunctions of the Qur’an, but also because if such an order were given it would not have resulted in the murder of a single Jew. 
Bashir Aḥmad M.A.:
After mentioning the account of Ka‘b bin Ashraf, Ibni Hishām has recorded the narration that after the execution of Ka‘b, the Holy Prophet instructed the Companions that now they should slay any Jew they were able to apprehend. Hence, one Companion by the name of Maḥīṣah, attacked a Jew and killed him. The same narration has been related in Abū Dāwūd as well. The source of both these narrations is Ibni Isḥāq. In light of the ‘Science of Narration,’ this narration is weak and unreliable, because Ibn Hishām has recorded it without a chain of narration, and the chain of narrators, which has been provided by Abū Dāwūd is weak and incomplete. In this chain of narrators, Ibni Isḥāq states that he heard this incident from a freed slave of Zaid bin Thābitra, and that anonymous slave heard this incident from an unknown daughter of Maḥīṣah, and that daughter had heard this incident from her father. Now any individual can understand that a narration of this type, where two narrators are absolutely anonymous and unknown, cannot be acceptable in the least. Moreover, even if a person contemplates in terms of Dirāyat, this tale does not hold true, because the general practice of the Holy Prophetsa categorically refutes the notion that he would ever issue forth such a general order. Furthermore, if this was a general order, then definitely as a result, there should have been numerous killings of this sort. However, narrations have only reported a single case, which substantiates that this was not a general order. Then, when it is established in light of authentic narrations that the very next day a new treaty was settled with the Jews, in such a case, it cannot be accepted at all that a command of this nature would have been issued. Furthermore, if such an incident had actually occurred, the Jews would have surely raised a huge hue and cry. However, no historical account demonstrates that any such complaint was lodged by the Jews. Hence, in terms of both Riwāyat and Dirāyat, this tale proves to be false. 
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 Ibn Hisham, Ibn Ishaq, Alfred Guillaume (translator), The life of Muhammad: a translation of Isḥaq’s Sirat rasul Allah, page 369
 A Critical Exposition of the Popular Jihad (Original 1885) – By Cheragh Ali, page 106 – 108
 Muhammad the Prophet: by Maulana Muhammad Ali, page 201 – 202
 The Life & Character of the Seal of Prophets – (Sirat Khatamun-Nabiyyin) By Bashir Aḥmad M.A., volume 2, page 294 – 296
So what about that story about rocks and trees denouncing a Jew hiding behind them so muslims could kill him? does hiding behind a tree equate fighting against muslims if you’re a Jew?
Hi, that has been answered in detail by scholars in the following article,