Yes, calibrating the wheels will almost certainly resolve this for you. For the record, here's the complete wheel calibration text from page 57 of the manual:
http://www.davesmithinstruments.com/wp-content/uploads/2015/06/Prophet-6-Operation-Manual.pdf?c90b2eCalibrating the Pitch and Mod WheelsIn general, the Pitch and Mod wheels shouldn’t require re-calibration.
However, if you experience what seems like a persistent problem with
either of them, the Prophet-6 has built-in auto-calibration procedure that
you can use to remedy the problem.
To calibrate the Pitch and Mod wheel’s low position:1. Rotate and hold both wheels in their low position.
2. Hold down the preset button and press 7.
To calibrate the Pitch wheel’s center position:• With the Pitch wheel centered, hold down the preset button and press 8.
To calibrate the Pitch and Mod wheel’s high position:1. Rotate and hold both wheels in their high position.
2. Hold down the preset button and press 9.