There's actually nothing in the original three that bothers me. They're classics, guilty pleasures. I think my least favorite part of Raiders must be the basket chase. In Temple there's not anything that bothers me. It's supposed to be wild, over the top, cheesy... Last Crusade didn't bother me either. It was for a long time the only Indy I was allowed to see. Maybe the broad daylight start and the comic beginning. Herman falling of his horse or Indy's horse taking a step right when he jumps. Though I thought that was a good one. It's a big difference though after everything that happened in Temple.
KOTCS, entire last forty minutes, including what Arizona Smith said. Marion being randomly hit by branches. And was the three time drop really necessary too?