This is a common problem and is easily remedied. But first I must ask this question, have you calibrated your machine axis? If your answer is NO then you need to perform this step and this screen is available using the ALT-6 key combination. It's a straight forward procedure whereas you select the axis calibration button located just above the RESET button.
I use a little test program to machine a 6 inch (my primary units) square and then actually measure the X and Y result. If it's of some value other than programmed select the faulty axis and simply enter the measured distance. Mach3 will adjust your motor steps to provide the desired outcome.