I recently saw a "too many comments" auto flag on a post which had only two comments on it at the time I saw it. It turns out that a somewhat heated debate had occurred about 40 minutes before the flag was raised, and that debate resulted in 19 comments. Another moderator deleted all the comments before the 20th comment was posted within the 3 day window. Then, someone else posted a new comment within that window and that immediately triggered the auto flag -- despite the fact that there was only one comment on the post at the time that the flag was raised.
Why does the system immediately raise a flag when the 20th comment is posted even if that comment is the only one left on the post? Why doesn't the system wait until a post has accumulated 20 comments visible to regular users within 3 days before raising the flag? Is this by design or an edge case?
I can see why it might be useful to flag for a moderator in the case where several users are continuing their previous conversation that was already deleted. Even so, that conversation might be useful and there's likely nothing for a moderator to do for the flag with just a comment or two on the post. Furthermore, it seems highly likely that some other user might come along and post an unrelated comment only to trigger an unhelpful flag (which is what happened with the post I saw).