I have NHL 16 on Xbox One and I've been playing BE A GM and like you guys I've had the same problems. I've had now three times that situation where I get a 5 min major for various reasons and I end up playing the whole game shorthanded after that penalty. It's not showing the clock for the penalty and the penalty just keeps going. First time it happened I was like "well I guess this is really REALLY RARE and it wont happen again!", second time it happened I wanted to throw my controller to the wall 'cause that glitch ruined my game and my goalies stats but I'm glad I managed to control myself and not destroy that controller. Today it happened third time and I pretty much just sat there quietly staring at the screen, playing the game through, defending my one goal lead and deciding I wont play this game before this glitch is fixed. It just ruins your game so totally.
The picture is from my last game where I was "lucky" to get the glitch in the last period, still managing to win the game and doing an empty net goal while shorthanded 6vs4.