Hello,
I'm facing similar problem . . . My wife and myself have both an iPhone 5, with same OS 9.1 and same settings, same provider (Proximus).
I'm charged a few times each month for activation sms sent to UK concerning FaceTime an Messages. My wife was charged only at the first use of the iPhone.
My provider also says that the problem is due to Apple, not to him. I finally discovered that they are right !
Since Apple's OS 9, when using Messages on several devices (iPhone, iMac, PowerBook, iPad, etc), you need to re-activate the iPhone (enter login and password) nearly every time after you used Messages on another device ! This activating is on billed !
Until now I never got an answer from Apple to this problem :-(
May be because not enough people are complaining about this story ?