This is a bug in the game I believe. It happens when you are right against the skybox, but the "camera" is behind it, causing things to disappear. I think the dev team said this is being fixed for beta 1.1, but until then, you can try putting a small (16 units possibly) wall in front of the skybox and apply the clip texture. This will make it so they see the sky normally, but they wont be able to move that close to the wall, and thus the camera shouldn't get behind the skybox. You just need to find the right thickness of your clip wall.
It's not something that can be fixed. If you move against the skybox, it's going to happen. It's due to the fact that the 'camera' has moved beyond the confines of where the map exists, thus the glitches. I don't know much about mapping, but one could probably surround the playable area with 6 invisible brushes to act as a boundary. Personally, i don't think it's a big problem.
Yes thats exactly what I was talking about Karrde. Along the edges of your map where the sky is exposed, create a brush and texture it with the clip texture (zhlt needed). It will create an invisible barrier so they cant get that close to the wall. We just need to figure out how big that wall has to be.