The game doesn't deal with offsides correctly - there have been loads of screenshots and recordings of the official making the wrong offside call, and yet after the complaint is made the game states that 'replays indicate the referee made the correct decision'.
Basically the are two possible problems.
The first is that the media engine and the match engine are unrelated - that the media engine decides that the decision is correct/incorrect based on something other than the actual incident - this could be the referee rating, for example.
The second is that there could be a problem with the match engine itself. The graphical display could be at fault (not displaying players in the actual position the game thinks they are in) or the match engine may not be tracking the back line correctly.
Either way though - it sucks and should be fixed.