Burned out motor controller
Sudden stops by the wheel, caused by running over small stones, will cause the motor to carve a notch out of the wheel. Check that the sidewalls are smooth and free of any notches. Sidewalls with notches or grooves can create clicking or knocking sounds. Notches are very hard on the motors and will cause significant loss of power. A tire with sidewall grooves will damage the motors.
Water or Static Damage
As long as the LEDs go on in sequence (Red, Yellow, then Green) at power up it means the the microprocessor is probably ok. I would think that the only things that would kill the microprocessor is water or static electricity (CMOS). But unless you drive through a lot of puddles, water won't get inside the motorboard, and there probably wouldn't be water damage.