The one I used to hate was if the ball was still moving in the in-goal and you touched it with one foot over the dead ball line, you got a 20m restart. I can't remember when this rule was introduced and removed, but Thank God the NRL got rid of that, as it completely robs the kicker of a good kick which either forces the player on the other team to either make a play at the ball (if it holds up in-goal) or touch it dead for a line drop-out.
The most famous moment involving this rule was Paul Carige in the 1998 Preliminary Final, which led to a line drop-out and gave the Bulldogs one more chance at victory in the final minute of regulation time because the ball had stopped when he touched the ball:
Likewise, a team getting a penalty from the half-way line after one of their players catch a kickoff with one foot out of the field of play should be scrapped too. If you do it on the dead-ball line, it should be a line drop-out and if on the sideline, a scrum. Kicks that are positioned in a way that forces the opposition to play at the ball should be rewarded.