Imagine how hot the PCB must have gotten 
dlovinger:
... it seems the consensus here is that there's protection against that and I can safely use VIN and connect to USB at the same time. I'll start doing this. ...
No, do not start doing this. Use only 1 power supply at a time.
I believe the OP used a 10A, 5 volt power supply. Not realizing how current/voltage and resistance are related they thought they were supplying 10 amps to the Arduino..
I usually take the batteries out when I use the usb. I’m pretty sure it actually discharges the battery faster using both. I haven’t researched this yet but it quickly drains cells. I think it tries to make up the fluctuating usb power.