Compass issue on latest firmware

We had an interesting compass issue with the latest copter firmware. We had one of our hexcopters (with many hours on it) try to fly away and display some weird flight problems. Pilot simply switched out of GPS mode and returned home with no issue.
After reviewing logs we found a compass issue with the 3rd compass. There shouldn’t be a third compass on here, we have dual Here3 and the internal compass is disabled, or so we thought. We discovered that even with the internal compass disabled in compass settings, it was still showing up in status. We finally did a compass_typemask and disabled all drivers except CAN and that seemed to eliminate the internal compass.
Is this a known issue or are we missing something? I certainly thought disabling the internal compass in the compass settings would be enough but apparently not. Any insight would be appreciated.

Can you go to the Mission Planner > compass calibration screen and see if the third compass is there?

You may remove unused compass there.