Is the device running iOS 10? That's a requirement for retrieving backtraces from processes running on the device.
If the device is running iOS 10, then it sounds like you've encountered a bug. If you could grab a sysdiagnose* from the device and your Mac when this happens and file a report at bugreport.apple.com, it would be much appreciated.
* Details on how to do this are available at https://developer.apple.com/videos/play/wwdc2016/721/?time=2441
I've just tried again with an iOS 10 iPad Air (1), and -- same problem. This is the setting I enabled:
Edit Scheme > Run > Diagnostics > Logging, Malloc Stack
Ran on the iPad, clicked into the memory graph debugger, and in the inspector under Backtrace, I still see "Malloc stack logging is not enabled for this process."
Anything else I should do or check?