Game management means plays are never looked at in a vacuum. A team that constantly walks the line may get warned by the ref to stop doing that, and eventually get called after a play that may not have been blatant, but because things have added up. "Stop doing that, Brad, stop doing it, I'll call you", refs never want to call a penalty.
A team may get away with one if power plays are favouring the other team, yet that other team is constantly doing a little stickwork/interference.
To the untrained eye, and to people who never reffed, it may seem like there are double standards or that there are makeup calls, but in fact the ref might just be trying to make the penalties match the number of infractions without having to call 40 penalties and making himself the star of the game.
The refs should answer to the players, not to the fans watching, and communication is key as to whether the players find the refereeing good. Most nights most players are happy with it. Fans are never happy.