Yes. How do you reconcile the Silver/Bronze Age Superman with the modern Superman's history? How does Lex go from being an infamous criminal to being the corporate villain Lex post Crisis? There's so much that contradicts in the Superman history it makes it very difficult to see how that can all happen in the same reality.
For other characters, like Batman and GL, it can work much smoother, but I think Superman's history pre and post Crisis is the hardest to reconcile. o