Open the included blend file (it's just set up so you can easily see the problem). In it are two meshes, a cube that has been extruded to have to different 'levels', and a flat plane with a mirror modifier. Also, Snap to Faces (with the project mode enabled) has been turned on. From top view, go into edit mode for the plane. Grab the edge that is on top of the cube, and drag it right. Because of the clipping from the mirror modifier, it doesn't move past the center. However, if you drag your mouse over the higher part of the extruded cube, the vertices snap to that height, even though they are over the lower part. I think what is happening is that you are moving the vertices to the mouse position, projecting them onto the surface, and then moving them back for the clipping. I think the process should be reversed, so that the vertices that are being clipped only snap to the surface that's under them at the clipping point.