For directions after seeing the sea snake: there are two rooms below that one (you can check the map if you're confused). The lowest of the two (do not go to the third, at complete bottom right) has a big water area with a bunch of lasers into it. Pass those lasers, scan the terminal on the top of that room, exit through the right and scan the terminal in the room just above. That will open the door and allow you to progress.
I'm still very clueless about those bugs to be honest, I've heard a lot of those cases and I'm still confuse as to why they happen. Will have to do further testing. Also exiting the water not being intuitive is known.
About the scanning mechanic: actually, the first thing you could scan were the spikes right in front of you in the first room. I get it can be too subtle, but I thought messaging the player that scanning stuff out of the ordinary gave you XP increasing your stats would be enough to push them to action. For the rest of the gameplay, do look for scannable stuff; hazards, warning signs, terminals and sometimes background props will definitely help you. If you feel you are short on health or breath, do go back to scan stuff.
In any case, thanks for playing and giving so much feedback!