If the parts you're cutting were modeled with the same program and sizes, then calibrating the machine won't necessarily help you. It'll just scale everything in the 3 directions, but the error should transfer to every part and cancel out.
What bit size are you using, and have you measured the true bit size? I have yet to find a bit that is exactly the size it's supposed to be. My 1/8" inch bits are usually .005-.010" undersized. Depending on how you're cutting (inside, on line, or outside line), the amount of error can stack up. The best way I've found to measure the bit size is to cut a single line and measure the width of it. Then use that for your bit size.
Another source of error may be lost steps, which is just another way of saying that the machine didn't move as far as it was supposed to because of one reason or another (loose pulley screw, loose/tight belts, tight V-wheels, incorrect pot settings, etc.). I don't know how long you've had your machine, but lost steps are a very common problem when dialing in a machine after assembly. There's a good forum thread here: https://discuss.inventables.com/t/guide-offset-cutting-lost-steps-positioning-errors-etc/16084
Having said that, you can calibrate various parts of the X-Carve easily. I made videos on calibrating the steppers, adjusting pots, and tensioning the belts, which you can find in this forum: https://discuss.inventables.com/t/x-carve-maintenance-troubleshooting-videos-add-your-own/13405