It can be a few things but sometimes that happens with under volting or clocking the min values such that the phone has difficulty waking from deep sleep. I had this problem on both AOSP and Sense 4.4.2 pretty consistently, but has not happened once since moving to even beta version of 7.0
I haven't tweaked any CPU settings and was running the stock kernel when it happened a week or so ago. Just to shake things up I ran the Elite Lunar Kernel. This weekend, I had it happen again. Should I try overclocking it?
Not a huge deal, but it can be annoying when you need to snap a picture, answer a text, etc.