I'm at the end of the Emporia level, just finished going back to the Salty Oyster Bar to complete the Sally quest, and can't open the turnstiles to move to the next level. When I approach them, a red message is displayed that says something like "cannot be used during combat." This made me think that there might be a straggler enemy to deal with, so I ran back to the Salty Oyster Bar and checked, but didn't find anyone.
I've run into this issue as well, in a later event. The game sometimes gets an enemy stuck outside the geometry, and in my case I could even hear him calling out to me. I searched the entire environment without finding him. I finally had to reload from a checkpoint.
I don't believe there's any way to fix this or work around it without loading a previous checkpoint, sadly.