I think the problem is mainly in the OT books. We do have alternate versions from the Dead Sea Scrolls of some books, with significant variations. Some books have seen significant additions (e.g. Isaiah - perhaps twice).
Aside from early editing (which we have some evidence of) the main problem in the NT is pseudonymous works (although there is an argument that the ending of Mark was lost).
And just as an aside this seems like an appropriate place to put this little comment.
A Christian fundamentalist is someone who believes that the Gospels four are independent accounts - all written by the same Person.