I've known this problem for a long time. In BG2 sometimes creatures "disappeared" in walls and then appeared again usually if you have gone to the wall from a certain direction...
Now I've encountered the problem during mod development. I was testing an area with enemies in it, a mine with narrow tunnels. I ran to two enemies, they attacked me but I ran away (I drank Oil of Speed). They tried to follow me but then stopped (this is normal so far).
When I have wanted to return to the point where they have attacked me, I (successfully) encountered them at a narrow tunnel -- but only one of them was displayed and only this could be killed! The other was also there but "in the wall". Actually not in the wall, but in a position where it could get my character stuck without noticing him (if my character had noticed him, the battle would have begun so the enemy could have been killed to free the path). But no, my character(s) kept trying to move but they were moving in one place because the "invisible" enemy's position prevented us in our path, it took our path.
The area's narrow paths should've been made wider while creating the area, right? There is no better solution, is it?
I thought of a CLUAConsole command which summons a wizard who offers you to ForceSpellPoint() some fireballs to certain points of the area -- so it would be RPGish but this idea is lame...
[Although it happened twice, I forgot to take a screenshot when I was really stuck. The example screenshots show the places where I was stuck, trying to make a model of the real situation.]