It doesn't help that Harbaugh goes crazy yelling at the refs anyway, so replacement refs seem horrible with all his antics, but they had several bad plays in the 49ers-Packers game.
Packers had a punt return for a touchdown but a penalty flag was thrown. Then the ref said that there was no penalty on the play. Looked like there were two blocks right near each other. The first was legal (but close to being in the back) and the second was pretty clearly in the back. The flag was thrown for the second, but somebody who saw the first thought it was for that and overruled it. That gave the packers a 70+ yard touchdown.
Earlier, Aldon Smith got a 10 yard sack and Rodgers' foot kicked his helmet almost all the way off. His hands took it the rest of the way and he got flagged for taking his helmet off, which gave them a first down instead of 2nd or 3rd and 20. And on the punt right before that drive, they called illegal block in the back on the 49ers even though they were the kicking team and the guy they called was the one who got pushed in the back (although it probably shouldn't have been a foul anyway). It's possible the penalty was earlier than the replay showed, but that was pretty weird.
The refs did miss an offsides call on the 49ers on a 3rd down play and they ended up getting the first down, so that was important and in favor of SF (and they got a touchdown on that drive I think).
There were a couple other close plays they got right. Several of the ones that Green Bay was mad at seemed like they were decent calls, and several other close calls against the 49ers were actually the right ones. But god it makes it harder to watch when you just have this feeling that they're going to screw up and do something weird.
Holy fuck I wrote an essay on replacement refs. I hope they get the real ones back soon so I can be pissed at them.