The fumble with Bowman wasn't really one of them. Yes in a fumble pile up, possession changes all the time under all those bodies. But there were a number of bad calls that would have been game changing:
1) Yes, 15 yarder where the hit to the head did not occur: bad call
2) 5-yard roughing the kicker on Andy Lee. Should have been a 15 yard penalty. Rule is if a defender hits the kicking leg of the kicker, its a 5 yard penalty. If the defender hits the plant leg, then it's a 15 yarder. The plant leg was definitely hit, which would have been a 15 yard penalty, which would have given the Niners a first down.
3) Ball spot. Seahawks 3rd down I believe, Lynch ran the ball and the Niners definitely stopped his forward progress well before the first down line. However, the officials marked the ball spot 2 yards past that point to give them the first down. My friends and I all saw it. What the hell was up with that!?!?
4) Intentional grounding. If I remember correctly, Wilson did this twice and no flag was thrown. He did get caught another time though.
Those were the ones that I can recall off the top of my head.
+1. Plus Bowman was simply on the ground, in possession of the football. That should have been the end of the story. Lynch's fumble rectified that call though.