Here is a complete project if you care to run this yourself: https://www.dropbox.com/s/5p384mogjzflvqk/AVPlayerLayerSoundOnlyBug_iOS10.zip?dl=0
This is a new problem
To expand upon Sami Samhuri's answer, here's a small sample project I worked up that uses a custom AVVideoCompositing class with custom instructions that implement AVVideoCompositionInstructionProtocol
https://github.com/claygarrett/CustomVideoCompositor
The project allows you to place a watermark over a video, but the idea could extend to do whatever you need. This prevents the AVPlayer bug in question from surfacing.
Another interesting solution on a separate thread that might help: AVPlayer playback fails while AVAssetExportSession is active as of iOS 10