Good question. The college problem is the biggest and most problematic, but there are a few other minor contradictions that are easily explained or ignored.
None of the three authors took especial care to be consistent with each other, though there aren't any glaring problems. I can't think of any contradictions with the movie trilogy, but since Young Indy was being produced concurrently with the novels, neither seemed to be aware of what the other was doing.
For example, I'm re-reading Genesis Deluge right now, and Indy's friend Jack Shannon is part of a small-time gangster family. They get beat up in a prison cell by Al Capone and his thugs, with no mention of Indy's contact with him back in Mystery of the Blues. Earlier Jack had to explain to Indy how Capone and Torrio had come to power in Chicago, even though Indy was there when it happened.
Phil