This is most likely caused by offgrid vertices, and since hammer has floating point precision loss, the vertices will not retain their original position when saving and loading. I usually get this problem when I make cones (spikes) or I use the clipping tool on a cylinder, but it can appear on pretty much anything that has a lot of vertices/edges meeting at one point (apparently).
In the screenshot I posted, you can see that if you zoom in all the way, in the bottom left view, the vertices (white dots) aren't on the grid. To fix the problem, I simply select the affected brushes, enable the vertex tool (

), drag a selection box and select all the vertices, then press
CTRL + B, to snap the vertices onto the grid.
However, sometimes the problem is so severe, that the brush becomes invalid. In that case, it's best to check problems with ALT+P, and see if there are any invalid solids. You can try clicking the "fix" button, but more often that not, hammer will stretch the brush into infinity making it invalid again anyway. It's best just to delete the brush and remake it.