If you home the machine, then jog to your starting point and reset the zeros. There is machine zero and work zero.
Check across the Y makerslide from back left to right front and from back right to left front with a tape measure ( kind of like making an X). If the machine is square, the measurements should be the same. If not, adjust them. Also When you home the machine, check to see if the X axis is square to the machine. The X axis can flex a bit, but when the motors are on you can’t adjust it. Some folks put a piece of wood in front of the machine and adjust it before they turn on the motors.
X & Y Not Square - How to Fix? - X-Carve - Inventables Community Forum