Answer by Rob on StackOverflow:
The problem would appear to be using “Recording mode” of “Deferred” when profiling on a physical iOS device, regardless of which Instruments template you choose. If you change the recording mode to “Capture last n seconds” (or, where available, “Immediate”), this problem does not manifest itself.
This problem jumps out at you when using “Animation hitches” template because that template does not accept a recording mode of “Immediate” and defaults to “Deferred” mode. But if you pick a different template, and manually change its recording mode to “Deferred”, that will also manifest the same problem.
Selecting "Capture last n seconds" instead of "Deferred" solves the issue.
I've submitted a bug report: "Deferred" mode should not be selected in the Animation Hitches template if it's not supported.