Did the shop power up and test the bike before trying to add the USB dongle? If it was working fine prior to that, my first thought is that the dongle had a manufacturing problem and was miswired or internally-shorted. Just plugging in one of those should be a low-risk no-brainer.
If designed properly, there should be no way to plug the dongle in wrong (notches, tabs and pin gender to make sure the connector is aligned properly before making electrical connection). Likewise, it should cause no harm to install a dongle with the battery installed, but the bike turned off at the controller - does the instruction sheet for the dongle make any mention of removing the battery before installing? (That would be a good idea anyway.)
Good luck and hope it works out quickly and easily, at least for you. Note that I have a MiniST with no dongle, so don't have firsthand experience with those.