Ardian Syaf, currently the artist for X-Men Gold, has been criticised for including the images.
Marvel fans pointed out that Colossus's shirt contained the words "QS 5:51" and, in another scene with new X-Men leader Kitty Pryde, a building had 212 written on it.
The references go against the company's inclusiveness policies, Marvel said.
It is also removing some artwork from the online edition of the comic.
QS 5:51 is a reference to a verse in the Koran, while 212 marks a protest on 2 December in Jakarta.