Guess this is intendet, since the car doesn't have a container to store loot, your gun will probably be thrown to the ground the moment you get in the car, like when you want to eat something.

But since the car was above the gun on the ground you didn't notice it.

Add a Gun Rack as a vehicle addon. If you've got a extra rifle in your hands when you get in, it's automatically stowed in the rack.

Yes, this is intended for now. The gun should get dropped on the ground when you get out from the car.
Obviously not ideal, we will try to think of ways to prevent this in the future.
Regards,
Andy