There is nothing there anymore in the Docks to use to exit the docks in either of the district exits in BGII.

It could be a modded "Dock" area and not the real one, and you're not supposed to exit it via the normal exits. Or could be some mods blocking the exits.

If you need help, please tell us exactly how you got to this point. What version of the game are you playing? What, if any, mods have you installed? Have any district exits worked for you in the campaign where these now fail?

Have you got a certain halfelf wildmage in your party perhaps?
She has a quest area that looks like the docks