I just watched every running play again. By my count, Johnson had a total of three negative plays out of 29 running plays.
There was one play when he slipped the nose tackle and tried to block the linebacker, but the linebacker used a swim move to get around him and stop Julius for a 1-yard gain. But there also was one play where he slipped the nose tackle, went out and blocked the linebacker, shoving him 6 yards back after contact (10 yards off the line of scrimmage), helping Julius pick up 13 yards.
One of the two other negative plays was the one when Johnson's foot got tangled up with Bledsoe's foot (it looked like Bledsoe might have stepped on Johnson's foot or ankle), and Bledsoe fell down as he handed off to Julius. When Johnson's foot got tangled up (or stepped on), his upper body got turned, allowing Adams to move them both along the line to the offense's right as the play got strung out. There were about four other 49ers who didn't get blocked, and Adams tackled Julius for a 1-yard loss.
The other one was when Adams got leverage under Johnson and pushed him about a yard back, Julius almost ran into Johnson's back, then got tackled by Bryant Young for no gain. The play-by-play credited Adams with the tackle, but it didn't look like he touched him.
There were a number of running plays where he took Adams or Sopoaga way out of the play, and he helped pave the way on four short-yardage conversions up the middle -- Julius' 4-yard run on fourth-and-1, Julius' 4-yard run on second-and-2, Polite's 2-yard run on third-and-1 and Julius' first touchdown run.