A player should get at least a game loss for playing with a squadron that wasn't exactly the same as the one they registered. You require players to submit lists to remove the possibility that they could change things round to round. Leaving off an upgrade and having an unaccounted for 3 points is reintroducing that issue. It is a situation that can be abused. That no one is coming forward to say the player used a different upgrade round to round is likely the reason it wasn't a DQ (and probable suspension from FFG) but that doesn't mean it isn't an error by the player that should have repercussions.
If a judge spot checked a damage deck mid round and found it to be incorrect, but likely not intentionally manipulated, that player is likely going to take a game loss for the illegal damage deck. You're suppose to bring a legal damage deck, there should be consequences when you don't.
You're suppose to play the squad you registered, and there should be consequences if you don't.
The rules clearly state that you are wrong.
"If a leader discovers a player’s squad list missing
appropriate information, he or she should find that player
immediately and update the squad list based on the cardsthe player is using. If this would result in a significant and
potentially advantageous change, the leader should consider
investigating for possible cheating."
The TOs should have considered investigating for possible cheating. That does not translate to immediate game loss.