I would guess that he omitted the one preventing anyone from apparating into the room. They have to get back in somehow in a few hours.
I think that's almost it. My bet is that the invisibility cloak detector is the missing charm. Harry and Quirrell are already in the room when they arrive for the first time, and as soon as they see themselves leave via Time-Turner, they take the cloak off and finish their meal before leaving. But yeah, they have to be in the room at the same time that a bunch of charms are on it, so they can't seal it off completely.
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.