I'm not sure how this is "secret". If you're using iCloud on your mac and your iPhone, and open up Facetime on the former, you'll see a call list (including regular phone calls, not just facetime). I agree it's undesirable that call history is sent to Apple - but it's pretty easy to notice if you use facetime across devices that the call history is synced.
Namely, Apple chose to provide this information to government surveillance when they could have (and indeed promised) to design it in a way that allows for the iPhone to be used in sensitive situations and by people who need security from state coercion and violence.