Worldcraft uses its own internal format with floating point values. When it's exported to .map, it rounds those values off, and sometimes rounds them the wrong way, so you get various brushes that are 1 unit off. Qoole has the same problem, but worse.
Aside from using floating point values for vertex positions, worldcraft also uses the wrong methodology behind brushes, I think. Instead of making brushes that are plane-based, it tries to do it vertex-based. This is bad because not all vertexes fall on the grid.
For example, say I have a wedge-shaped brush that's 1 unit tall and 2 unites wide:
one unit tall
v
.
| \
|_____\
^ two units wide
If I split it, I'll end up with a vertex that's halfway between gridpoints:
half a unit
v
| \.
|__|__\
If these brushes were done in worldcraft, when you exported the map, it would round the vertexes to the nearest unit, and you'd end up with something like:
.__.
| |\
|__|_\
Or:
|\
|_\
I haven't tested this theory yet, but I'm pretty sure worldcraft would screw it up. I've been noticing more and more misaligned brushes in your maps, DT, as they've become more elaborate. I think it's time for you to take off the training wheels and use a big boy map editor.