This issue need to be addressed in the OT-2 app.
Upload your protocol to the OT-2 app
When calibrating the your desired labware, calibrate to the top, and lower your pipette just slightly lower than at the top of the well. If you find your pipette is 1mm off from touching the bottom, then calibrate it 1mm lower than the very top of the labware.
Attempt to do a run without any liquids/reagents in your well - this will allow you to see if the tip is going to the desired position.
Did the tip go where you needed it to?
If yes - then next time you calibrate - do not change anything. The robot will remember your previous calibration for the labware - so you do not need to adjust it again - you can trust and confirm that it is in the correct place.
If no - then adjust it again slightly - relative to where it went to during your trial run. Once saved, attempt a run again without any liquids.
This process should enable you to get the tip positioned to where you need it to land.
Please note that once you have achieved the correct calibration positioning - you no longer need to calibrate that labware type again. The robot will hold on to that calibration and have it stored in it's memory.
If the above did not solve your problem
Email us the file at firstname.lastname@example.org so we can take a look.