HI Seynin,
Thanks for the reply. We can certainly try that, but it's not the whole answer. While I was reading your reply, my wife was using her iPhone next to me while plugged in (the iPhone, not the wife), and three notification bong sounds occurred without any screen notification whatsoever. We looked at the notifications list and there were none. I asked my wife to unplug the phone, wait five seconds and plug it back in again and there were two bong sounds in succession. The battery level was at 100%.
I design embedded electronics and software for a living, and this has all the hallmarks of a software defect. It is clearly intermittent, so is likely related to complex interaction between several different processes and features, which makes it hard to find. But a defect this certainly is, and there are ways to identify the defect and fix it. Given that it's waking up many users regularly in the middle of the night, this should be receiving a higher priority from Apple. If Apple can't fix it, then I can suggest people who can. PM me, Apple.
Anyone from Apple iOS development care to comment?