I am also having the same issue.
My problems only occur AFTER exporting via AME. I am working on a video rip with sound effects and Voice overs layered on top of each other. The problem (as far as I understand) comes up when the sound effect comes in – at which point the VO glitches and randomly repeats a part of itself. I tried exporting VO and SFX separately (which made it worse actually, the glitching became more frequent), I tried fading in the SFX levels and it didnt work.. Here is what it looks like on my timeline:

I’ve tried exporting it as an aiff, exporting to audition, restart my premiere and computer, updated to 9.2. I am literally out of options and the deadline is looming.
I’m on OS X EL Capitan
10.11.1
Processor: 3.5 GHz 6-Core Intel Xeon E5
Memory: 16 GB 1866 MHz DDR3 ECC
Graphics Card: AMD FirePro D500 3072 MB
Working on .mp4 (no issues in the past) and exporting as ProRes files.