Overall I think the refs did a good job with this game, and I didn't ever feel like we were being screwed like in 2005, though I was worried before the game that it might happen.
On Russell's run, when he placed the ball on the ground before going out of bounds (I'm assuming this is the play the OP is referring to), it was obvious to me that he was still a couple of inches short, so even though it was a valiant effort, it didn't bother me at all.
On Sherman's play where he gets mugged, I also didn't have a problem with the no-call. If anything, I was relieved that he didn't get called for DPI. We all know that OF COURSE it wasn't DPI, since he was looking at the ball, etc. - but that's the kind of play that refs can get wrong and just "assume" it was pass interference.
Also, I honestly don't think Sherman was going for the INT. I think he knew exactly what he was doing, getting in front of the receiver, slowing down to keep the receiver from getting to the ball, all while looking back for the ball as if he's going to catch it, but knowing full well that all he needs to do is prevent Thomas from getting to it - mission accomplished.