It actually happened on the first level of my second playthrough. I was thinking maybe I squished the bug too fast? Also there were times when some bugs would not spawn at all (or do they not spawn on the cracks?). The game thought I squished the bugs though so it was fine.
I played it in Edge. Regarding the bugs not spawning, I think the same thing happened during thatmanrobin's stream (but I don't think he paid much attention to it so I'm not sure if that's intentional).