Well in the part of the film when Woody & Buzz are riding RC back to the moving van, Woody is controlling RC with a remote control. Then when RC runs out of batteries they use a match to light the rocket & they speed up to the van, but RC's control is not there from the time the batteries go dead right up until they drop RC right in the van
Woody drops it when he goes "great!" And Andy probably ordered a new control, thinking it had gotten lost while moving. You can order controls and parts for R/c cars, you know.