@bbriggstkd said in Warning: motor phase A (or B) may be disconnected:
The only wires that are on are the LED +5v and LED VIN.
Sounds like something is broken I'm affraid. Your 3.3v LED should light up if you have USB or Vin connected (as well as the 5v LED which does work).
Pull the SD card out, see if anything is getting hot; wifi module, CPU or regulator U2.