You probably have to calibrate the machine a bit closer to your desired specifications.
Check out my 3rd post in this thread. The other possibility is flex in the machine. Make sure the wheels are tight but not too tight., and that the belt is tensioned. These machines do flex some too due to their construction. Check that calibration with an accurate caliper or machinist’s scale.
Calibrating my X-carve 1000 - X-Carve - Inventables Community Forum