I've done a lot of work with a sleep machine app, these clicks were the bane of my life.
I discovered they were being caused when the android audio system comes alive, I solved the problem by permanently having a sound playing at zero volume, this forces the audio manager to stay alive, and will stop the clicks. Not a very elegant solution, but it works.
The sleep machine, I designed it to play at very low volumes, even re-sampling to decrease amplitude, as you can imagine the clicks were very noticeable, and completely destroy the purpose of most android relaxation apps.
https://play.google.com/store/apps/deta ... e.lullabye