I’ve been constantly having to move vertices back into place and I don’t know why.
When I saved my map about an hour ago everything was in place.
I saved my map, quit hammer and source sdk, then I played ep2 for a while.
Now I open my map again and vertices in random places are off the grid.
It means that one of the the faces is not coplanar. When you re-load vmf, it’s automatically readjusting it for you. Do not ask how to disable this feature, I do not know and definitely would not want to. Actually, doing so will cause much worse consequences.
Like Sirrus said, try redoing that brushwork with the clip tool this time.
The reason the vertices keep getting misaligned is because the brush you are making is very slightly concave, and Hammer can’t work with concave brushes. The brush may not look concave, but when the vertices do this, it means it is concave.