I can't reproduce the car returning the flametumbler. Same for locomotives, all locomotives i tried returned the ingredients and nothing else (don't know which train mod you are using)
Mining the flametumbler returning the car is correct, since the car is an ingredient in the flametumbler recipe.
Can you upload a save somewhere ? Even a freshly started should do, just so that i can test it with all the same mods you are using. There might be some unexpected mod conflict.