Could be many things
As a signtist you have to do some
Troubleshooting
The same could be said about all equipment and operations in a sign shop
Unlike printers these machines are pretty simple and usually do what there told to do.
When I am cutting all the way through I usually go at least .06 and cut into a sacrificial sheet.
First thing I would look at is the toolpathing.Is it correct?
Is it operator error ?
Forgot to zero properly?
Zeroed from the bottom and should have done top?
Wrong bit for the job?
Is the table not flat?
Is there something wrong with the machine like a loose spindle?
Does the machine ever have a problem cutting within .020 ?
Did you first check all the obvious?
This list could go on and on and on.
Hope this helps and you solve your problem