A person accidently killed Miqyas’s brother. The Prophet (p) gave Miqyas blood money to resolve his brother’s accidental death. Miqyas accepted the money but later murdered his brother’s killer. One must take note here, the person who killed Miqyas’s brother did so accidentally.
In contrast, what Miqyas did was pure treachery, by killing someone unlawfully despite accepting blood money. Miqyas knew if he stayed in Makkah he would be killed for the crime he has committed, he ran away and joined the polytheists and became an apostate.
Miqyas ibn Subabah
Miqyas b. Subaba came from Mecca as a Muslim, so he professed, saying, ‘I come to you as a Muslim seeking the bloodwit for my brother who was killed in error. The apostle ordered that he should have the bloodwit for his brother Hisham and he stopped a short while with the apostle. Then he attacked his brother’s slayer and killed him and went off to Mecca an apostate. 
Islamic Scholar Taha Jabir Alalwani
MIQYAS IBN SUBABAH AL-LAYTHI
The reason the Messenger of God ordered this man killed was that he had murdered a man from among the Supporters (meaning the Ansar, the Prophet’s supporters in Madinah) who had killed his brother by accident, then returned to Quraysh as a polytheist.
Al-Baladhuri states, ‘As for Miqyas ibn Subabah al-Kinani, he had a brother by the name of Hihsma ibn Subabah ibn Hazn who had become a Muslim and had taken part in the Battle of Muraysi with the Messenger of God, during which he was killed accidently by one of the Supporters, who thought that Hisham was one of the polytheists.
Miqyas came to the Messenger of God, who ruled that he should receive blood money from the paternal relatives of the Helper who had accidently murdered his brother Hisham. Miqyas took the blood money and declared himself a Muslim. Thereafter, however, he assaulted the man who had killed his brother and murdered him, then fled as an apostate, saying,
‘It gratifies the soul to have spent the night in the trench, One’s robes spattered with the blood of the treacherous.’ Hence, the Messenger of God gave orders to anyone who met up with him to put him to death. The reason for this was that he was a murdered, someone who broken with his nation and community, and joined enemy ranks. The sin of apostasy in this case was followed by a crime. The order given by the Messenger of God to kill Miqyas ibn Subabah was not due to his apostasy; rather, it was a form of retribution for the person he had murdered. 
Sealed Nectar – Ṣafī al-Raḥmān Mubārakfūrī
The other man who was put to death was Miqyas bin Sababa. He was a Muslim. A helper accidently killed his brother Hisham. The Prophet (p) had arranged the payment of blood money to him, which he had accepted. His revengeful nature, however, was never appeased, so he killed the Helper and went to Makkah as an apostate. 
 Ibn Hisham, Ibn Ishaq, Alfred Guillaume (translator), The life of Muhammad: a translation of Isḥāq’s Sīrat rasūl Allāh page 492
 Apostasy in Islam: A Historical and Scriptural Analysis By Taha Jabir Alalwani, page 50 – 51
 Sealed Nectar By Ṣafī al-Raḥmān Mubārakfūrī page 397