What material were you using?
This often occurs because the material is not perfectly flat on the honeycomb bed. Many of us use the hold-down pins (below) or magnets to make sure the material is not lifting up anywhere.
if you are not using proofgrade material, there is also the chance that you have entered the material height incorrectly, or that there is a hidden obstruction in the material (like a knot or an inclusion in plywood… see here: Inspecting thin plywood for voids and glue)