Hmm. The headphone jack on an iPhone/iPod Touch can accept a three-ring plug where the extra contact point is used for input from the headphones to the phone, instead of the other way around.
It's used for headphones that have a microphone and/or a
remote control on them, and it is how it is able to listen to the signals from the mic and/or remote.
Does this random occurrence only happen at the moment that you plug the car input into the headphone jack, or can it happen at any point while you are listening to music from the phone? Sounds like for some reason the phone is interpreting something that it is "seeing" from the car as remote control inputs. If it only happens at the moment you plug in, it's probably nothing to worry about...the iPhone is probably seeing something short or discharge briefly in the jack (static build-up, maybe?) and thinks, based on the characteristics of whatever it sees, that you hit the pause or track-next or whatever button on the non-existent "remote" on your "headphones."
If it is happening randomly during the course of your ride, that is a bit more worrying, since it suggests that there could be some power coming from the stereo over the input wire to the phone, which there shouldn't be. Does the mini-plug on the end of the input cable have 2 black rings going around it, or 3?
-- Nathan