I only listen with headphones. I have several, wired and bluetooth different brands. It happens with all. What confuses me is that sometimes I can restart with anyj heaphone control but some times I must tap the phone and then touch the app play arrow. The app is there so I just start play again. This started with the lollipop update.
I use Overdrive and OneClick digital. for library books, Audible for purchased. Mostly I use my old iPod touch for music as android music apps are seem to be based on streaming, purchasing with no timed off ability. Itunes is easier to use by far for music and old audio books.
I have searched the web since it started before my question to this site. The problem is common and so far I believe unsolved. I am awaiting Marshmallow from T mobile.
I would recommend Google Play Music for your music playing needs. I've had no issues with it when it comes to controlling the music player via headphone controls. As for audio books, I couldn't say as I don't play them.