We have experienced the same thing! Our Tech, had the internal power on the mini-prog active, and an external source active at the same time.
We also met similar issue before, my experience is:
(1) Avoid short Miniprog3 Vtarg to GND of target board or vice versa.
(2) Avoid power the target board use external power source and Internal power source at the same time.
(3) Don't plug Miniprog3 with target board after target board is powered up.