The Prophet (p) ordered Rifa’ah bin Qays to be killed because he incited other tribe(s) to go to war against the Muslims. This is reported in many sources.
THE RAID OF IBN ABU HADRAD AL-ASLAMI ON AL-GHABA TO KILL RIFA’A B. QAYS AL-JUSHAMI
One whom I have no reason to suspect told me from Ibn Hadrad as follows: I had married a woman of my tribe and promised her two hundred dirhams as a dowry.
I came to the apostle and asked him to help me in the matter and when I told him the amount that I had promised he said, ‘Good gracious, if you could get dirhams from the bottom of a valley you could not have offered more! I haven’t the money to help you.
I waited for some days when a man of B. Jusham b. Mu’awiya called Rifa’a b. Qays or Qays b. Rifa’a came with a numerous clan of b. Jusham and encamped with them in al-Ghaba intending to gather Qays to fight the apostle, he being a man if high reputation among Muslims and told us to go to this man (T. and bring him to him or) bring news of him, and sent us a old think she-camel.
One of us mounted her, but she was so weak that she could not get up until men pushed her up from behind, and even then she hardly managed to do so. Then he said, ‘Make the best of her and ride her in turn.’
We set forth taking our arrows and swords until we arrived near the settlement in the evening as the sun was setting. I hid at one end and ordered my companions to hide at the other end of the came and told them that when they heard me cry ‘Allahu Akbar’ as I ran to the camo they were to do the same and run with me.
There we were waiting to take the enemy by surprise or to get something from them until much of the night had passed. Now they had a shepherd who had gone out with the animals and was so late returning that they became alarmed on his behalf.
They chief this Rifa’a b. Qays got up and took his sword and hung it round his neck, saying that he would go on the track of the shepherd, for some harm must have befallen him; whereupon some of his company begged him not to go alone for they would protect him, but he insisted on going alone.
As he went he passed by me, and when he came in range I shot him in the heart with an arrow, and he died without uttering a word. 
Ṣafi al-Raḥman Mubarakfuri
In the year 7 A. H., shortly before the Compensatory Umrah (lesser pilgrimage), a man called Jashm bin Mu’awiyah ( or know as Rifa’ah Bin Qays) came to a spot called Ghabah where he wanted to gather the people of Qais and entice them into fighting the Muslims. The Prophet (p) in hearing these reports, dispatched Abu Hadrad with two men to see the situation.
Abu Hadrad, through a clever strategy, managed to rout the enemy… 
 Ibn Hisham, Ibn Ishaq, The life of Muhammad: a translation of Isḥaq’s Sirat rasul Allah, Page 671 – 672
 Sealed Nectar – Ar-Raheeq Al-Makhtum: Biography of the Prophet By Ṣafi al-Raḥman Mubarakfuri page 379