I've noticed a lot of peculiarities with the way the Y cable and iPhone interact. I think the bottom line is that BMW's implementation of the iPod Accessory Protocol doesn't play very nice with the much, much newer iPhone.
One thing I've noticed is that any time the music player subsystem control changes hands (for example, from the built-in music app to Rdio or Pandora), bad things happen and the car gets confused. My rule of thumb is to plug in the cable once my app of choice has already taken control of playing music.
As for email incoming and whatnot, I haven't experienced problems yet. That definitely wouldn't be related to a defective cable, though.