The "Because We Scan: Vents" (Scan everything in the Vents Region) achievement didn't unlock. I unlocked everything else (including scanning everything in the game ("Because we Scan"). I thought that the intermediate achievement didn't unlock.

However I went back and found some non-fish that I hadn't scanned (a drill bit, a couple of inactive vents, and something else). So apparently either Because We Scan was bugged (unlocked too early) or more likely, it actually only requires scanning all of the living things.