I really don't think the refs do anything intentialy. It's simple human error. All of the action on the court takes place in a split second, and as anyone who watches a game on TV knows (from the multiple angle replays), what you actually see can depend heavily on what angle you have on the play. The refs can't only make calls on things that they are 100% certain about or there would never be a whistle blown during the game. I think at the end of a game, a series, the playoffs, and the season (especially) that the calls that go for and against you really do even out.
Sure, I'd love it if a refs call never decided the end of a game (i.e. by putting someone on the line, fouling someone out, etc) but it's just not realistic. They'd have to be ordered to swallow their whistles for the last two minutes. If that happened there would still be plenty to complain about.
I think the thing with the refs that annoys me the most is when coaches and players get fined for complaining and criticizing the refereeing. I think it's ridiculous that these guys shouldn't be held publicly accountable. I'm sure there is plenty of review and chastising that goes on behind closed doors, but this is public entertainment, this isn't a private club, or a secret society, let these people speak their minds about what they're seeing, that's exactly what the refs are doing when they blow a whistle and make a call, I think the coaches and players should be allowed to publicly question the officiating with out being reprimand and fined for it.