Joker
Not to criticize Matthew Modine but Joker is a very annoying character. Not to say that Modine may not have done the role justice but given Kubrick's reputation for beating what he wants from his actors/actresses I can only imagine that Joker was meant to be that way.
For example, during the filmed interviews in Hue... Just the way he rambled on and quoted some very poor cliches about war in an attempt to be humorous. It just didn't come off well. It felt fake. Maybe that was the intent but it just seemed so forced. His confrontation with Animal Mother was also another point where I just wish he'd have shut up and gone away.