"The red apple is in the car."
Translation:A piros alma az autóban van.
The difference is that your version sounds natural. :) "... az autóban van" is how you would normally say it. "Benne van az autóban" sounds to me like the apple is a part of the car, and it is built in, it is inside. Or that it is included. Like tax in the posted price.
Maybe it is just me.
Another version is "bent/benn van az autóban".