We are looking at this issue. But because of its intermittent nature, we are unable to reproduce the issue.
Can you share the sample files with which you are facing the issue?
Are there any specific softwares installed on your system?
You can mail me the files and information at firstname.lastname@example.org
I have the same issue in CS6. This guy had it in CS5.5 way back in 2011: https://forums.adobe.com/thread/792075 It is ridiculous that Adobe have not dealt with it yet (they can forget about me 'upgrading' to CC).
I got around it by clearing font caches every day (using Smasher and/or Font Nuke) and switching ligatures off where I could. I had the problem with Goudy OS and Frutiger opentype fonts. It is not a problem that I can reproduce short of wondering if a file has lots of styles and some have ligatures enabled and others disabled.