Nolan,
It sounds like you are using makerverse and a due. Are you using 1.0.6? Without wanting to use edge or precision (hole) calibration in version 1.1.2, you need to go back through Makermade’s calibration process of making the square and adjusting the factors for 1.0.6. Otherwise @dlang is right: you have to do the calibration. there is a video for 1.1.1g which is close enough to 1.1.2 precision calibration with holes… calibration link in this post.