Whoever did it would have to remove the rear wheel and disconnect the motor. there's two problems that can come directly from that, which could cause your problem: Firstly, they didn't push the connector in far enough, which is a very common problem; secondly, they might have damaged the motor cable where it comes out of the axle if they were careless or not used to working with motor wheels.
There are other problems that could have been caused indirectly or are not related at all and just happened coincidentally. If you hadn't mentioned the gears being changed, the pedal sensor would be second on my list after the motor sensor, like Neal explained above. Next on my list would be the brake switches, which can self activate if the cable is sloppy or can be switched inadvertently if you rest your fingers on the lever while riding, but as that didn't happen before the gears were changed, that's not very likely.