Malcolm commented on an early post on this subject and may have put his finger on the issue:

The issue is likely latch-up due to a deviation in design from the the original Nordic development board from which the micro:bit is derived. The micro:bit has two processors, the main Nordic and a second (NXP/Freescale MKL26Z) used for USB programming and comms.

To reduce power consumption, only the Nordic is powered from the battery supply whilst the USB supplies both. A potential issue is when powered by battery only, the Nordic can place voltage on some of the GPIO pins of the MKL26Z whilst it is un-powered.

So far not a issue, but as soon as the USB is plugged whilst the battery is still connected, the MKL26Z powers up. Powering up a chip when voltage is already present on input pins is very bad and usually results in ‘latch-up’ and a very hot blown processor.

He has also pointed out an un-official circuit diagram of micro:bit.