Jim Harbaugh yells at refs. Like, a lot. It's in his nature. He's like this even off the field, as exemplified at a Citrus Bowl promo event, wherein Michigan and Florida players competed against each other in physical challenges, like in game shows such as Minute to Win It.
It was during the final event, where players wore belted boxes around their butts and had to shake out balls in said boxes. Harbaugh went full Harbaugh and yelled at the game show host for awarding Florida instead of Michigan, and then demanded a redo. Shaking balls out of a box with your butt is serious business:
HUGE controversy on the final game. Both sides claim victory. Florida called the winner, but Jim Harbaugh storms the stage, demands a re-do.— BWW Citrus Bowl (@BWWCitrusBowl) December 31, 2015
You can see from the slight smile on Harbaugh's face that it was all in good fun. Ultimately, Florida won the whole thing, by proving they can shake their asses better than Michigan:
The Citrus Bowl between Michigan and Florida takes place on New Year's Day, and it's guaranteed that 1) Harbaugh will yell at a ref and 2) he'll actually be pissed when it happens.