On the surface, it would seem like a book like A Wrinkle in Time would go largely unnoticed as far as the "Banning Books" crowd goes. There does not seem to be anything particularly controversial, especially when compared to some of the other novels we have read this semester. But apparently, the aspect of the book that is most cited as the reason for its removal from the public view is its descriptions and references to magic, specifically in the form of fortune telling, as well as having Jesus listed among a number of other influential individuals. While there does not seem to be a lot of official explanation for some of these arguments, one could assume that concerned parents did not want their children being exposed to the concept of witchcraft in any kind of positive light.
It's safe to assume that these were likely the same people who had a problem with books like the Harry Potter series, who likely retain some view that witchcraft and magic are real phenomena, are inherently evil, and should be stamped out of all public discourse. But it also particularly interesting that they seem to hold the view that A Wrinkle in Time is in some manner anti-religious or anti-Christian, considering the fact that the author, Madeleine L'Engle is herself a Christian, and attempts to convey a somewhat Christian ideology through her writing. She is not unlike C.S. Lewis in this regard, who uses a host of Christian imagery throughout his Chronicles of Narnia. L'Engle does not seem to be as overt, and utilizes more aspects of science fiction in the work, but the symbolism is clearly present.
It would seem that there are two explanations for this criticism of L'Engle: That her work is not religious enough, or that it is too religious. There was apparent dispute over listing Jesus among a number of other influential persons in the novel. One possible way to view this criticism is that concerned individuals did not want Jesus being portrayed as just another member of a particular club, but rather being above it. But another potential criticism could be that concerned individuals simply did not want children being exposed to religious content in a nonreligious environment. Obviously this argument is somewhat less believable, considering the fact that much of the book has religious content that is inspired from both ancient and contemporary practices, and Jesus is only one of several religious figures who are mentioned in the course of the novel. But it is conceivable that just as someone would want to control the kind of religious messages children read about, it is equally conceivable that someone else would want to prevent children from receiving any kind of religious content at all. Both are, in this writers opinion, equally wrong to try and assert their personal will over this conversation, but it is nevertheless a conversation that will remain controversial.