On teachers: The initial system was designed around one teacher per subject I think, there were a bunch of minor bugs if you assigned multiple (not sure if the Keller chain was a play on that, and is just an artefact of that). I think most of the issues have been fixed by now, and there's further control with being able to pick the subject + room in schedule. Basically teachers struggled to tell which subject/room they were meant to be in if same subject was taught at the same time by multiple people (that also had other subjects) - so you'd end up with multiple teachers in one room, or no teachers at all (because they thought the slot was filled and they were free).
Squark Uh, pregnancy has been redesigned a lot in terms of logic since the public version. Does she only have the trait? If she doesn't have the Status Effect (Pregnancy) then that's probably by design (the message not clearing bit was a bug, but harmless).
Unless she still has the Status Effect, she simply decided to have an abortion. Hypno/rape results in the NPC not knowing/hating who the father is, so they have a choice to abort/keep depending on personality/if they have someone else to bring it up with. She also might've chosen to keep it, but won't inform you - in which case something might be wrong with her stomach.
You can check if the child exists by running, in the Database tab (FatherID would be either 0 (PC) or -1 (unknown)):
Code:
SELECT * FROM Children WHERE MotherID = (her UID from debug) AND Born = 0