Well, I finally got to make and finish a map, thanks to alot of utilities downloaded from this site, and I'm still very proud of it, but it's extremely glitchy.

Example

Could anyone show me how to fix this?

And I gave credit to CMT in the video's description.

When something has a imprecise bounding radius, it can cause a player to move through scenery or the bsp itself. Have you ever flown a wasp down a small corridor, and you can see through the walls and sometimes if the walls are thin enough you find you can move through them? That's what's happening here. Vehicles and other things are hard to construct tight bounding radii for. That's why custom vehicles cause more glitching than say, a scorpion. You're not going to be able to fix the bounding radius, though, it's really difficult and demands specific skills. Hopefully you can find another work around. Does this glitch happen with a traditional biped? I've had this happen, but it was due to a turret having an exit animation and bounding radius that placed the player below the bsp. I "fixed" it by raising the turret to make it float in mid-air.

No, it hasn't happened to the Spartan biped. Just the Brutes. I would test other bipeds, but I'm still getting all of the files to use them.

Then it must be the biped's bounding radius. Unless you're proficient with 3DS Max, I would suggest using a different biped. Not everything that CMT released in their tagset works properly. The covie shade, for instance has problems with its physics

I don't even have 3DS Max. But this tagset is pretty much just for decorative idle Brutes, considering I found no actor variants. But I'm going to finish getting all of the Elite files. Elites are better anyway. :p