I would simply list all merits and flaw without categorization, not even into mental, social, physical, etc.
I don't think doing so creates any real issue, and it's up to each ST to set the houserules or review character sheets, at least merits and flaws, to ensure weird things don't take place. Even if they do and he hasn't checked before, if he believes a character has no business having a certain merit or flaw, he can require the player to change it when he realizes the issue. It's annoying sometimes, but it's the game.