Since I updated to OS X El Capitan a few weeks ago, I’ve only had one significant software issue.
My advisor from the University of Michigan, Professor Jason Corey, wrote a book about Technical Ear Training a few years back. The book is great, and it also includes a fantastic software package he put together for training your ears.
I set aside some time each week at work to use this tool, and it’s really helped me keep my ears focused over the years. I fired it up the first week after updating to El Cap, and the icon just bounced around in my dock forever.
Jason built the tool in Max/MSP as a standalone application. I’m not sure what changed in El Capitan that impacted Max, but he was able to fix the issue just by rebuilding the tools (on Yosemite, I believe).
He posted version 1.02 as an update on his website. According to the license, the software is available for noncommercial education and research use, and I highly recommend it. Download it, and if you enjoy it, buy his book!