After Jerry Gourd plugged the plug under the table into the outlet to power up the ship, the lights turned from yellow to white, but at the shot of Scooter, the lights are still yellow and then switch back.
The USS Applepies is not moving at all (in space), and is supposedly out of power. It should have been moving at whatever speed it was moving when it lost power, because there is no friction in space (so it couldn't have slowed down).
The USS Applepies can't move out of the way of the meteor because it is out of power. Bob and Larry's ship is shown to be fully functional, however. If Bob, Larry, and Junior were able to enter the Applepies from it, it would have to be latched to the Appliepies. So why not just use the smaller ship to get the Applepies moving?
If Jimmy & Jerry really ate the popcorn meteor, they would've increased in size. They're seen hitting the ship windshield at their regular sizes. Additionally, their mass would be approximately equal to that of the meteor, yet the USS Applepies is not destroyed. The glass that they hit is not even cracked.