I'm glad you enjoyed!
The very first enemy will chase you no matter what, the trick is to lead it back into the spike trap - but we could've possibly explained that a bit better
Every other enemy follows the 'as long as you haven't made a noise or touched it, it can't see you' logic, and that's where the crouch mechanic comes in!
As far as the story goes, think of the 2D cutscenes as the prequel events that led to the creation of the laboratory. It would've been nice to have more in-game items tying it all up, but we were already stretching ourselves pretty thin by the end of the 7 days
But thank you for playing it and leaving us some feedback!