In the room with boxes: the broken wall/door/whatever has 2 overlaps, a thing on ceiling above boxes has 2 overlapping. Just outside the room: ceiling corners. On other side of the broken wall the sloped floor overlaps with wall on one side. The box around the whole map each corner. The smaller box around most of the map has loads... etc. These are just the ones I took time to find and list. In many places you have more detail stuff overlapping.
Detail brushes overlapping shouldn't cause VIS problems, but can cause texture problems IIRC.
Basically start selecting everything and move the camera around. Imo the easiest way to get rid of all, is to lock textures, move a section of the map out (use largest grid size), fix it, next section.
You also have some things that should be detail but are structural: the wall with door behind the boxes should be detail, with a caulk structural wall behind it. Same with curved ceiling above boxes.
EDIT: All your curved walls/ceilings are spsed to be detail. Especially the broken curved ceiling... And the room behind broken wall from the room with boxes (and there is a tiny tiny weird angled structural brush in there...) When you compile, you also get a .prt file which you can load with plugins->prtview, then toggle 3D/2D portals. The alien base has some major overlapping brushes near the entrance to box room...
