This is an error that DJI knows about. It is in their firmware and will hopeful be addressed in the next version that will be released soon. It isn't caused by the Map Pilot app. Map Pilot doesn't actually control the flight at all and relies solely on DJI's waypoint navigation functionality.
We have referred to this internally as "bucking". It appears to be doing altitude adjustments every second or so and adjusting quickly upward even though it is fairly close to the target altitude.
You took the appropriate action. We have done A LOT of mapping and it has happened on on off for entire flights without actually causing any issues. It is certainly a little unnerving though.