Walls are off by a few units.
Add clip brush.
I only took a quick glance I think you could do 20X better on the cave as well looks like you rushed it almost.
Lol....
You said the cave looked fine before, now you say it's rushed...
The 2nd screenshot is meant to be like that, I have never bumped into it after rushing through the cave 20 times, there's no need for a clip brush there. & the 1st screenshot doesn't show up like that in bsp, it's less than 1 unit - unfixable, it's the angle.
Aside from this clipz, the cave is on about 30deg angle, so not all brushes line up properly. I spent 2 hours doing this cave, if it were straight (not on an angle), I could of designed it 10x better in half the time.
ALSO. The map has far too many brushes as it is, r_speeds hit 3k in some places, adding more brushes will bring some computers to their knees. (even after adding hint brushes, there are just many polygons in one area... and the angle doesn't help at all)
Don't forget clipz, this isn't quark, BSP has no good working functions that I can rely on, can't easily rotate things.
Another thing, I have made this rock-cave-transition twice, so in total 3 hours working on it. The 1st time, It looked MUCH better, but the compiler wouldn't take it and stopped responding every time I tried to compile. The only thing that had changed was the cave - when I took them brushes away, it compiled.
Not to sound rude or anything, I will not release another beta unless something worth fixing arises.
In my next map, I'll go for a less complex layout, it will still have much detail, but less angular.