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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.