One of the new features in OS X El Capitan is a new security mode called SIP that doesn't allow software to run on a root level. While that's a great security feature, it has been messing with certain software. If you want to get a glimpse of what isn't working, MacIssues shows you how.
If you head into your Applications folder you'll see a cross through incompatible software, which is a handy way to see which app might need updating. But that doesn't really show you what SIP is blocking. For that, you'll need to dig around in some folders.
Head to: Your HD > Library > SystemMigration > History > Migration-UUID > Quarantine Root (UUID will be a string of numbers related to your computer, not the letters UUID). Here, you'll find a list of components that don't meet El Capitan's new security protocols. Unfortunately, it's not as simple as a list of apps, it's just components, but you should be able to troubleshoot from there.