Did the whole thing a second time for good measure. Could not reproduce glitching through the floor this time.
It is a fun little mission as an opener to a series, although I have 2 small nitpicks:
The plague section felt a bit empty (I get why, from a story perspective, but just a little bit more player engagement would have been nice).
General thing regarding scripted events (issue in several missions, I think): Plan ahead for what you don't expect the player to do (which sounds a little contradictory, now that I read it). If there is an event the player might want to tweak in their favour and you suggest to the player that the option exists, that option better work.