identically placed brush FACES (with textures) can sometimes go wrong, but then you should never end up with that situation normally anyway.
I think that s a bug. I get that sometimes too, its when the same brush in exactly the same place twice. I tracked it down to a screwing-up of radiant when using Ctrl+Z, but it does happen seldom, probably when u ve been working in radiant for a while without saving the file.
