I'm starting this thread to list the issues:
1. Otis (the well-fed security guard): Helmet is missing (i.e., no back of head), and no arms or hands. When shot and killed, the hands appear but the arms don't
2. Some of the human grunts don't have heads (Map 11, after you enter the building where the tramway starts)
3. If you blast the Vortigaunt with a grenade, it (presumably the corpse) appears as a standing Vortigaunt (Map 11, after the stairs at the end of the tramway)
4. Otis' name appears to have changed. I can no longer summon him with his original name - "Otis01"
5. I can't be sure, but the Beretta seems awfully high-powered. I was able to gib a Vortigaunt with a few shots
6. If you warp to a map, the player starts with a crowbar instead of without a weapon