I have 1000 hours of gameplay and this never (?) happened.
The map is a summary of submaps, overlay them and voila you can get any kind of not working maps, especially with the same layer, which would otherwise be impossible.
Not as far as I know. It's one of the explicit checks in submap generation, that there should always be a space between a door and any wall. Really no idea how this happened
I can of course come up with a backup fix that prevents the game from freezing should this somehow happen again. A weird door would be a minor bug by itself, it's the freeze that is problematic.
Or rather, the map itself was bugged, causing this.
See something strange in that shack? The door opens into a wall. The door is originally closed in the save, and there's an alien on the outside side of the wall. He wants to run into the shack and then gets stuck at the door. Tries to open the door as usual but fails because somehow there's also a wall in the same tile. I have no idea how that happened in the first place.
You're on Steam, right? Just switch branches - right-click the game in your Steam library, choose Properties, go to the Betas tab and choose "community" there (no password needed). That will give you the best installation of X:CE, which also updates automatically. I think that's the best starting point.
An already frozen save? No. X:CE might salvage it due to being much more stable in general - I've fixed several "freeze in combat" bugs in X:CE.
If the save doesn't work even in X:CE, I might look at it and see about making a fix.