Since the GE doesn't consider time passing during shots or rebound struggles, it may have been an off-ball foul during rebounding struggles. Actually, there doesn't seem to be another option. I have also seen this type of fouls, sometimes on the defender and sometimes on another defender off the ball. So technicly it's not a bug, just an unrealistic feature of the GE. The shot clock only ticks during possessions, while in real life, it also ticks during the shot itself and rebounding struggles.
One big and main bug that I've seen, and I'm sure everyone have seen, is the one that after the 24 second shot clock expires on a team, the game clock keeps ticking away, sometimes for 10 seconds or more, until a turnover occurs or a foul is called. Now THAT is unrealistic AND buggy.