During a protocol run, when the pipettes move to labware, you might notice:
One pipette goes to the correct place.
The other pipette is up to 1-2 mm off, and that error is consistent throughout the protocol.
Why this happens
This is a known limitation in software versions earlier than 4.0.0.
On the OT-2, labware is only calibrated with one pipette. To move the other pipette to the same position, the OT-2 relies on knowing the exact offset between the two pipettes' tips. It measures this with pipette offset calibration. (See How calibration works on the OT-2.)
Before software version 4.0.0, the OT-2 took that measurement by automatically tapping its pipettes against five tip probe switches hidden under the OT-2's trash bin. This could be inaccurate and imprecise. So, whichever pipette you didn't calibrate labware with would be slightly off-position when it moved to that labware during your protocol.
How to fix it
If you still see this problem after updating, reach out to Opentrons Support.