Have you followed the librepilot setup wizard as you dont have to actually calibrate the ESC’s as you just tell librepilot the values that the motors start to spin, so each motor will probably be different and its not a problem. This is explained at around 7:00 in the video below
If you want all motors to be the same the best way to do the calibration is to plug the ESC directly into your receiver as we explain in this ESC calibration guide