When the coyote falls through the hole on the bridge, he pulls a trail a dust and road debris down the hole in his wake. When the scene cuts to the long view, the trail is not seen following him down.
When Wile E. Coyote has the magnet around his waist and he is chasing after the Road Runner, he follows the Road Runner down some train tracks. The magnet would automatically be attracted to and stick to the metal of the train tracks, not continue to follow the Road Runner anymore.
When Wile E. Coyote is falling off the cliff with the bow in his hand his body seems to go thru solid rock but the bow somehow doesn't and hooks itself on the rock.
At the end, Wiley rides a rocket into outer space, past the moon. The rocket explodes like fireworks, and the flares all fall in the same direction, as if the rocket exploded on earth and gravity pulled them toward the ground. But there is no gravity in outer space, and the flares would travel in straight lines away from the center of the explosion, like the ripples of a rock thrown into a pond.