I have been having issues with the iPhone 4s too. At first I used it has BT audio device and then started mangling with the iPod connection since it seemed to offer better control. When I turned off the car and started again a few minutes later with the phone still hooked up to the iPod connector it seemed to be stucked on PAUSE, so I hit play, it restarted but with no sound at all. After switching to another audio mode and coming back I believe this is how I got it to start working again... I will try a few different combinations and post detailed information. Maybe it doesn't like being on BT and iPod at the same time, I will disable BT audio on the car stereo and see how that helps.
Otherwise I am pretty satisfied with the Phone integration and the hands free, I used to have a BT thing connected to my AUX on my VW and used SIRI for voice recognition, had to repeat phone numbers a few times before she got it right, but the CX-5 voice recognition understands me every time.