MB3 126b: Trapping Flies and Bees on Shabbos (316:3-5)

Closing a box if there might be a fly/bee inside on Shabbos. Stepping on ants on Shabbos unintentionally. If an animal is trapped right after you lay the trap it's an issur d'oraita.

Spreading a covering over a beehive.

If a deer enters a building on it's own and you close the door afterwards.