OS X El Capitan comes with a brand new security feature called System Integrity Protection (SIP) where certain system processes, files and folders are protected even from user with root privileges. Prior to El Capitan, root user or user with root privileges can tampered with any system resources.
SIP, also dubbed ‘rootless’, reduces the security risk factors of OS X significantly. It also means that software and apps that store their files on system folders are not allowed anymore. When you upgrade to OS X El Capitan, OS X will block those apps and move them into a special folder.
The folder is located at Macintosh HD > Library > SystemMigration > History > Migration-xxxxxxxxxx, where xxxxxxxxxx is a string of characters unique to your Mac. Within this folder you’ll find all the software files that are quarantined by OS X El Capitan. The files are not as simple as a list of apps but is a good place to start troubleshooting and to identify those apps you missed upgrading to be compatible with OS X El Capitan.