Di2 Rear Derailleur Troubleshooting with Rear Wheel
The derailleur may be auto shifting because the Di2 system overshifts slightly to make the shift faster and smoother, especially at the extremes of the cassette. Then it settles down into the right position a couple of seconds later.
A new wheel set is what can cause a problem. The position of the cassette left to right is slightly different on each manufacturer’s hubs. So, every time you change wheel sets you should re tune the rear derailleur. With a new rear wheel, the cassette can sit slightly further inboard then with the previous wheel. Just reset your limits and tune your indexing and you are good to go.