What age group?
I've had really new Juniors put down a stage 2 as their starting Pokemon when they are just learning to play. I'd give them a caution, and would then help them start the game correctly.
If you are talking about an experienced Senior or Master Division player, it sounds like the player is intentionally committing an infraction to gain an advantage. That meets the description of Cheating (7.6.4 in the Penalty Guidelines) and should result in a disqualification. If the hand really was a mulligan, the player would have a difficult time arguing that their actions were not intentional.
If the opening hand really wasn't a mulligan, the offending player may be able to argue that they were rushing the setup, and grabbed the wrong card by mistake. If that was the case, I might lower the penalty. I'd want to talk to both players to try and get a good picture of the situation.