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@IlmariKaronen: I have a lot, but after a bit of tedious binary searching I narrowed to down to balpha's stackapps.com/questions/3894/dude-wheres-my-cursor (although I still don't know exactly how that interferes — there are no error messages). Sorry to bother you with a report that turned out bogus.
@IlmariKaronen: i.sstatic.net/6rlle.png for example, or I just footled around taking out one or two of the opening characters of a comment, putting them back in, and waiting until the warning showed up.
HTML comments trigger the "Bad HTML that will be silently removed" warning, which is dumb, since they're supposed to be removed. The parser doesn't actually support them directly, so this is understandable, but an irritating glitch all the same.