I assume the mesh is solid (3rd construction method), and you're sure of the elevation.
Check for geometric inconsistencies such as contours crossing. Is the mesh a target of any solid element operations? Try canceling the ops, and check the operator elements for inconsistencies too. Lots of ops on a mesh can eventually lead to trouble. I never cut the mesh with the actual foundation walls, I place a slab(s) for the sole purpose of cutting the grade. It's an extra step, but more reliable.
Meshes can be very glitchy, especially as they become complex, and sometimes they fail for no apparent reason. If you can't find the offending condition, gradually simplify the mesh by (
) deleting contours one at a time, and checking the section. Assuming it fixes itself, try to restore what you need.
The mesh tool is crying out for an update in features and reliability.
HTH,