#9: Just watched the replay and as soon as the return was blown dead, the 40 second clock started and never stopped. Unless I'm misinterpreting the rule, it should have been a 25 second clock and should have started when whistled 'ready for play' by the ref. The same thing was also happening on extra points even though they are 'after a score' on the list below.

If the officials signal the Game Clock to be stopped for any of the following reasons, the Play Clock
shall be set to 25 seconds, and will start on the Referee’s signal:
-Penalty administration -Charged Team or Media Timeout
-Measurement -Team B is awarded a 1st down and will next snap the ball
-After a kick down -After a Score
-Start of each period -Start of a Team’s possession series in an extra period
-Instant Replay review -Other administrative stoppage