This also happened to me. I've had bulkheads in my base for a couple of days now, but today, when I loaded the game up, the bulkheads just won't open. I guess you'll just have to get rid of them, at least until the next update
EDIT: I just closed Subnautica, and loaded up the same save, and the doors still did not work, but when I tore them down, and replaced them, they worked just fine
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EDIT: I just closed Subnautica, and loaded up the same save, and the doors still did not work, but when I tore them down, and replaced them, they worked just fine