I was assuming it was something to do with python, as far as out of order stuff so far aside from the 2 I already mentioned, there was another one where you talk to azalea about rag reading the farming book before you actually give it to her, I haven't reached act 2 yet so I can't speak on further sequence breaks for now
edit: just did act 2 and your first event with clint sounds like you've already completed experiments despite only needing to clear the act 2 mission to access it