On Neptune's Bounty I had just got the camera and death-warped to the fishery. I skipped all the dialog, the door opened, but when I went to go in the guy said "you're fucked" and the door slammed shut and I was unable to enter.

Has this happened to anyone else?

The "You're fucked" is earlier dialogue and it is just playing it then but if you cannot ever get him to open the door even after the dialogue has finished it means you did not get all 3 pictures of the splicers.

The door opened, but it closed before I could get in. I took all the pictures

Without a clip of it, it is really hard for me to say as I can't say I have had that happen or ever seen it occur. If it happens every time you do the level could you record it from the start?

It only happened once and I have no idea what caused it. I'll post a clip if I can get it to happen again