First of all, this is an issue that needs to be addressed by the WMs.
Cards should not be included in a deck that the player themselves cannot play.
However, there should be NO PENALTY for this, as it didn't affect the outcome of the game at all.
The problem is that it could be abused, where the sub could have the Marks, but not the original player.. especially if there's no way in knowing if the original player has that amount of Marks or not.
In conclusion, there should be no penalty, but the rules should be amended to address this.