When the boys are christening the "Thunder Road," Ethan Hawk's character tries unsuccessfully to break a beer bottle on it. Then after they each take a drink from the bottle he throws back over the space ship into the creek where you here an exploding sound and glass breaking. The sound of the beer bottle breaking is actually the sound of a light bulb be broken. A beer bottle would not make a popping sound like that because even if were under pressure from the carbonation of the beer it would have to be in a vacuum, which it isn't. Light bulbs implode rather than explode causing the popping sound due to the vacuum they are in. The beer bottle should have sounded more like a small window being broken.
When Ben and Darren walk over to Wolfgang's house, Ben is wearing brown corduroy pants. Then when they go down to the basement, he's wearing blue jeans for a few shots. And then he's back to wearing his brown corduroys for the rest of the scene.
During the hill scene, Wolfgang creates 2 holes in the ground. One leading downward while the other ends going up exploding a large hole near Darren and Ben.
At the end of the film they are back at the same hill and there is no sign of the hole near the tree trunk Wolgang came out of.
During the maiden voyage of the Thunder Road, Wolfgang removes his glasses and puts them in his jacket/shirt pocket before putting on his gas mask. After putting on the mask his glasses are back on underneath it and he is not seen putting them on.
At 07:16 on the DVD, "2517 Davana County School District" is written on the side of the school bus, but at 49:58, the sheriff's helicopter lands by a sign reading "Davanna County" and at 50:51, deputy Gordon reads a copy of the "Davanna County Gazette".
On the maiden voyage of the Thunder Road, right after the sphere-field activates, the camera cuts to the front of the ship for a brief second and a half, and we can see the boys, mainly River Phoenix in the middle, waving their hands very enthusiastically and out of character for the scene. It's possible that this was an outtake that was cut into the film by mistake. Joe Dante has always said that due to studio pressure, the film released is basically a rough cut.