I have run into this a few times with the OSEPP pro mini where I have external 12 vdc connected to a 6 vdc regulator then to the raw input of the pro mini. I was using the serial as well for loading and serial monitor . I noticed the regulator was getting hot ( I always do the finger scan over the board to see if anything is getting warm ) . I will go look at the schematic to see what I did to correct this as I have made a few other projects as well since where I corrected this and was able to monitor the circuit while it was live with external wall wort.
BobD