Wow I just arrived here to say exactly the same. I obtained the Elevator Gate Key and just opened that gate door with it, but it is as if the collision data doesn't match with the visual data.

Closing an restaring the game does *not* solve this.

Btw this is the first issue that can be considered a bug in this game. I find it remarkably bug free: I've experienced neither crashes nor glitches. Oh, a few hours ago I could run with the Armour on, as if I had my normal clothes on; I suppose that is an issue.

It's been resolved in the latest patch:

IMPORTANT: If you try to go through the open metal gate in the Harbour and you're blocked by an invisible wall, please go around via the Northern Slopes or the Shore and you'll be able to cross that gate again (the invisible wall will disappear automatically).

http://store.steampowered.com/news/?appids=417290

Strange way to "resolve" this. Mention a workaround (haha) for a bug is not resolving it.
Figured it out by myself.

Unfortunately this happened to me today, so it is still not fixxed....

Well, I´m playing the game today and the thing with the harbour door is still bugged. This is annoying AF since the bug got so many years...

Same happened