Presumably it has an error catcher that outputs ‘DO NOT MESS WITH TIME’ when this happens.
That message came from Harry, not from physics. Roughly speaking it indicates that a stable loop where Harry gets hysterical is easier to arrive at than a stable loop where the problem is solved. ie. In one of the instances something surprising and dangerous but non-fatal (would have) happened so that (potential) Harry would have set up a stable time loop that prevented that branch from ever happening. (Or maybe Harry just went paranoid for no reason - hard to tell with him.)
Everything that comes from Harry comes from physics! But of course I really mean that it outputs something to deter the agents in question from trying to push things that far. In Harry's case, that's ‘DO NOT MESS WITH TIME’ in scratchy letters; in somebody else's case, that's something else. But the simulation should be able to calculate whatever is needed.
Update: Discussion has moved on to a new thread.
The hiatus is over with today's publication of chapter 73, and the previous thread is approaching the 500-comment threshold, so let's start a new Harry Potter and the Methods of Rationality discussion thread. This is the place to discuss Eliezer Yudkowsky's Harry Potter fanfic and anything related to it.
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. The fanfiction.net author page is the central location for information about updates and links to HPMOR-related goodies, 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: