Are you using brushes or patch meshes for the terrain?
If you're using brushes, there are probably some invalid brushes, so you should run a brush cleanup (You may also need to close and reopen Radiant for it to work properly). In future, try not to edit vertices as much as you can, since the vertex editor in Radiant is very very buggy. Whenever possible, edit edges instead.
Also, if it's any help, EasyGen may help you generate terrain more easily too.
If you're using patch meshes, make sure the mesh is facing the right way. I recommend against using patches for terrain, though, because the game physics has a lot of bugs that allows players to clip right through.
I have no experience with any other method of making terrain.