I thought that the intermittent glitch was there being two Harry Potters, when he's using the Time Turner. Though, theoretically, they should have noticed this before, given that Harry's not the first student to use one.
The permanent one could be that the name Tom Riddle is constantly juxtaposed with Quirinus Quirrell.
Time Turners and the Marauder's Map didn't mix in canon works. Double entry glitch seems likely.
I can't recall, did canon works show Harry in the Marauder's Map despite being under his invisibility cloak? I would assume from dialog in HPMOR that it wouldn't be able to detect him as it's ability to hide is such that he can elude even death's detection.
Update: Discussion has moved on to a new thread.
The load more comments links are getting annoying (at least if you're not logged in), so it's time for a new Harry Potter and the Methods of Rationality discussion thread. We're also approaching the traditional 500-comment mark, but I think that hidden comments provide more appropriate joints to carve these threads at. So as of chapter 67, this is the place to share your thoughts about Eliezer Yudkowsky's Harry Potter fanfic.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six. The fanfiction.net author page is the central author-controlled HPMOR clearinghouse with links to the RSS feed, pdf version, TV Tropes pages, fan art, and more, and AdeleneDawner has kept an archive of Author's Notes.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: