El Capitan is incompatible with CS6. It may work with some features and not others.
CS6 is now four years old, and is considered end-of-life. It will never be updated.
Roll back to an earlier MacOS version, or upgrade to InDesign CC (subscription).
We get postings every day from CS6 and earlier users running into problems under El Capitan or Sierra. It's just the way things are.
Okay, thanks, I'll probably have to upgrade to InDesign CC soon. In the meantime, I'm working around this problem by getting simpler URLs at bitly.