The most common reason for a toolpath to cut deeper into the material than designed is due to the Z-axis bearings hitting the top travel limit. When this occurs, the machine still thinks it has gone the distance that it needed even though it physically did not, resulting in the Z-zero position being lower than initially set. In the Vcarve/Aspire software, please go to Material Setup on the right-hand side of the screen on the Toolpaths tab and select Set. In the bottom two boxes, there are two settings that control how high the machine will raise up, the Z1 Clearance and Z Gap Above Material. These settings need to be high enough to clear any clamps the bit might encounter while traveling from one cut to the other but not so high the bearings hit the top travel limit. Changing the "Rapid Z Gaps above Material" Z1 setting to 0.25" and the Home/Start Position Z Gap above Material to 0.25" should resolve the issue you are experiencing.
Please also view Vectric's digital manual for more information on the Vectric Material Setup Definitions.
When you start the file, please watch the bearings, circled below, to make sure they do not come into contact with the top plate.