Intermittent one is either people using time-turners, Weasley's don;t know about time-turners, so they think it's showing one person in two places or If it showed two names for the same person, that might be an intermittent bug too, ie Quirrel/Riddle based on who he is at the moment.
Permanent bug might be someone floating in the castle who they know shouldn't be there, perhaps Pettigrew, or Sirius, or someone who should be there but isn't - ie Quirrell being unplottable.
Dumbledore & Snape are known Occlumens, but they show up on the map just fine.
In canon, the bug that Harry saw was Pettigrew on the map but he wasn't actually there in reality.
I don't think either of the glitches are Time-Turners. Time-Turners have (presumably) been used regularly in Hogwarts since the twins arrived, and it's made clear that these glitches are new:
The Map was an extraordinarily powerful artifact, capable of tracking every sentient being on the school grounds, in real time, by name. Almost certainly, it had been created during the original raising of Hogwarts. It was not good that errors were starting to pop up.
(The HPMOR discussion thread after this one is here.)
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. There haven't been any chapters recently, but it looks like there are a bunch in the pipeline and the old thread is nearing 700 comments. The latest chapter as of 7th March 2012 is Ch. 77.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author's Notes.
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, seven, eight, nine.
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: