Re-watched the game. I put all the questionable calls (and some correct calls) in this video.
The foul on Bonner's three (2:07 mark): Looks like it was a foul, but I'm disappointed that the always reliable Fox Sports Houston did not air a replay there. From the standard live cam, it does look like Martin got Bonner. Stupid foul.
Parker loses ball out of bounds (1:43 mark): This too looks like the correct call. What do you think? The Rockets were upset, claiming the ball went off Tony Parker's knee. It didn't. Lowry swiped it and though you can debate that Parker touched it last, that call is usually made the way it was. Parker's ballet-slash-shot-out-of-a-cannon move after the fact was funny.
Courtney Lee Charging Call (2:24 mark): I think they got it wrong, but it's not an easy call at all. I think Lee was at a disadvantage because he was a little out of control and was going up against four guys. Still think it was the wrong call ... one that went to the hometown team because it's probably a little easier.