I think the problem with it is that it was supposed to happen before Raiders of the Lost Ark, but a lot of the things in Raiders don't make sense in that context. Like, I heard someone remark that it was weird for Indy to say he didn't believe in all that "superstitious hocus pocus" after the events of ToD. Unless, of course, he was just trying to make himself sound braver.
That, and it's completely ridiculous how, in the scene on the rope bridge, there's a gaping river in some shots, but you can clearly see in the wide shots that it's just a puny stream underneath them.