So there is a bit of inconsistency with the rules - it depends on where the ball goes as to whether a live offence has been committed. Instead, the rules are more along the lines of having a punishment, but not too much.
Bit of devils advocate here - if the penalty is not scored, an indirect free-kick is awarded to the defending team. According to your definition, the encroachment has been made when the game is not live. Perhaps it's more that when the ball is struck, the game is live, and the other attacking...
Well they didn't have a goal disallowed, the had a penalty retake disallowed. So add them to the long list of teams who've been denied a penalty. At least it didn't cost them any points.