After installing the latest beta release of El Capitan, I discovered loud clicks and pops when listening to any kind of audio (iTunes, YouTube videos, etc.) through my DragonFly external DAC. I reconnected audio to my Mac Mini's headphone jack and the clicks and pops disappeared, then reconnected the DAC and they returned, so I am assuming the speakers, and cables are not causing the problem. I also switched in a different DragonFly DAC I use for my laptop and got the same pops and clicks, so it does not appear that I have a faulty DAC, but that the problem exists within the beta's audio itself.
El Capitan Beta 2 introduces clicks and pops to audio when using external DAC
A lot of people have noticed this. The result of lots of device sync errors. Two bug reports have been filed already (that I know of alone).