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.
"The mentioned artwork in X-Men Gold #1 was inserted without knowledge behind its reported meanings," said Marvel in a statement.
"These implied references do not reflect the views of the writer, editors or anyone else at Marvel and are in direct opposition of the inclusiveness of Marvel Comics and what the X-Men have stood for since their creation.
"This artwork will be removed from subsequent printings, digital versions, and trade paperbacks and disciplinary action is being taken."
In Indonesia, the numbers 212, 51, and QS 5:51 relate to a series of protests against the Christian Governor of Jakarta, Basuki Tjahaja Purnama, who is currently running for re-election.
Last September, Basuki was widely criticised after a speech in which he claimed that Muslim groups were using a verse from the Koran to oppose his candidacy.
There were large-scale protests from the country's conservative Muslim population who called for his arrest on charges of blasphemy against Islam.
The biggest one was on 2 December, 2016, hence the term "212."
It's not clear what disciplinary action will be taken against Ardian Syaf, who is currently expected to be involved with future issues of X-Men Gold.