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No. Simon Magus is in fact mentioned in the Acts of the Apostles (see chapter 8), and this did not prevent the text from making it into the cannon.
The Acts of the Apostles was received into the cannon because it was considered a credible text based upon apostolic testimony. For example:
The Acts of Peter has none of this going for it, and appears to be a much later, more embellished text, versus the studious historical account provided in the Acts of the Apostles
Upvote:1
None of the individual acts of the various apostles was included in the New Testament. The usual reason for not accepting scriptures such as this has to do with whether or not it was written by an apostle or a direct disciple of an apostle. Our Book of Acts is attributed to Luke, thought to be a disciple of Paul. But in this case, there is no such claim in the text, although there is a tradition that and it was written by Leucius Charinus, whom Epiphanius identifies as the companion of John. So the argument for its apostolic origin is rather weak. By the way consensus among academics reportedly points to it being based on the Acts of John, written in the second century.
I find no reference to the reason why the Acts of Peter was not included. In fact there seem to be few references to it in the early Church Fathers generally.
This leads to the question of popularity: how widely was it read, especially in churches? The Acts of Peter was not nearly as entertaining or well-written as popular apocryphal acts such as the Acts of Paul and Thecla, and the Acts of Thomas. It may simply have been not well known as the others and in any case would not have competed well with them.
I do not see anything in its description of Simon Magus that would disqualify it. A better candidate for a problematic passage is either his conversation with a talking dog (ch. XII) or his miraculous resurrection of a herring (ch XIII). Simon Magus was already well accepted as real. Talking dogs and resurrected herrings, not so much.
See Acts of Peter here for surviving text.