Boris FX has not yet qualified Media 100 Suite for Mac OS X 10.11. Media 100 Suite v2.1.6 should be considered "beta" software for this new Mac OS. For those who are willing to try v2.1.6 with El Capitan, please report feedback on the Media 100 Facebook Group or at Creative COW. When testing beta software, we strongly recommend setting up a test system, and not installing the software on a system you are counting on production.
Media 100 Forum on Creative COW
There is a known installation issue that occurs when freshly installing Media 100 Suite v2.1.6 under Mac OS X 10.11 (El Capitan). Boris FX is aware of the issue and they are actively investigating it. The error does not occur if Media 100 Suite v2.1.6 is already installed on your system before you upgrade your Mac OS to El Capitan.