SAMD21J18 abnormal boot
The booting is probably an independent issue from the wake problem. To troubleshoot the booting problem, a debugger for the booting code would be best. 

Somehow your triggering the wakeup circuit on the MCU. There are two ways this could happen, one is with ESD, the other is the internal circuitry of the MCU has been damaged by ESD and the transistors are easily triggered.

If your not wearing an ESD strap, you probably should. It's not surprising that touching the case of the oscillator triggers transistors on the MCU, your sending thousands of volts through the case of the oscillator (or wherever the pin is touching), and a small amount of current. This current flows indeterminately through PCB, and could cause transistors to trigger on the MCU.