If your printed models are out of scale, in any axis, like it happened to me with the Z axis -you can clearly see in the picture that the hole looks like an oval instead of a circle- you might need to calibrate your firmware stepping parameter.
In the Marlin firmware there is a define called DEFAULT_AXIS_STEPS_PER_UNIT containing four factors corresponding to X, Y, Z axis and E (extrusion). Re-calculate the new steps using the following formula:
new_steps = (expected mm / actual mm) * old_steps
Compile and upload the firmware to the 3D printer.