Mark a picture might help and you can post pictures from your computer.

What design software are you using? What control program are you using?

Might be as simple as using the wrong post processor when saving the cut file.

Try cutting a square and see if the measurements are correct. The larger it is the better, this will tell you if there is a problem with any of the measurements. Also, check the angles and make sure they are 90 degrees.

Try cutting an arc across the Y axis and see if it also has the flat on the top like you describe.

 

Sounds like you have some backlash on the Y axis lead screw. See if you can manually move it back and forth a bit. If so, then a coupler may be loose, or the drive nut may have work down.