It would not happen, if there where a correctly working automatic vertex-snap tool.

The walls are simply either overlapping, or having a small crack between,
since the vertecies are not on "integer" numbers.

The light-mapper / calculation of the static lights works actually
quite good, if the level is build properly.
But the way WED lets you edit blocks in the "standard" way will lead
to unclean alignment.
You can best check that by opening the level-file in a texteditor
and have a look at the vertex positions, they are very often
on numbers like 45.4403 or so, it should be 45 when modeled correctly.

Its partly to blame on WED and partly on the level-designer.