After Clay Matthews hit Colin Kaepernick late, out of bounds, that led to a mini brawl in which 49ers LT Joe Staley was penalized for unsportsmanlike conduct, offsetting with Matthews late hit on Kaepernick. Referee Bill Levy explained after the game how he incorrectly enforced the penalty
“On the play where the quarterback (Kaepernick) went out of bounds and was hit late out of bounds, and then there was a subsequent hit by a San Francisco player, the down should have counted,” Leavy said. “The penalties were both dead ball and they should have offset at the spot where the runner went out of bounds. And it would have been fourth down.”
The 49ers then scored on the following play on a TD pass, where they may have gone for a field goal if it was 4th down. This was a pretty big error to make in the first week of the season.