I've also had this problem, though I just bought Deadfire yesterday, so it's always been this way.
What *seems* to happen is that the navigation map ends up offset from the drawn map on the screen - say, as if you moved everything that blocked movement 5 meters up the screen as an example. The direction varies, but I've definited noticed the obstructed areas (they end up with the O with a line in it indicating an invalid location) tend to be shaped like nearby obstructions.
This doesn't let you move through objects, however - it just removes areas as valid movement targets.
I find if I screw around a lot moving characters individually I can eventually get through, as generally speaking the obstructed areas only apply to individual characters, and they're often in different places for different characters.
I had the entire center area of the "Eye of the Kraken" blocked for half my party earlier today; had to go to the upstairs entrance to be able to go upstairs at all as a result ("You must gather your party to proceed" except Xoti and my Watcher couldn't walk through the middle of the room)
I find when it gets bad, you also see NPC's pathing get screwed up. I witnessed this in the Huana village at the first port, where one of the workers got stuck vibrating a couple meters away from the ramp he appeared to want to walk up.
Either way, it's tremendously annoying, and leaving and re-entering that screen doesn't fix the problem.