@Ottobawt the calibration process assumes that the bed is flat, the towers are parallel to each other, and the Z probe has the same trigger height at all point. If one of these conditions is not satisfied then calibration may indeed result in not printing to scale and square, especially if you use 8- or 9-factor calibration.
If the bed is aggressively textured, then using a large number of calibration point will help because it will tend to average out the lack of bed flatness.
Alternatively you could put a flat glass plate on top of the bed, run calibration, then remove the plate and adjust the calibrated homed height by the thickness of the plate.