Sorry to hear that you’re having some problems.
As Martin mentioned, Cubase 7.5 is not supported by Steinberg on OS X 10.11 - Cubase 8 has just been made compatible via an update which solves a similar problem some users were encountering with that version with Focusrite interfaces.
If you’re not intending on upgrading to Cubase 8 in the immediate future, a workaround that we have seen to fix this issue on a number of systems is to create an aggregate device is OS X. To do this, go to Applications > Utilities > Audio MIDI Setup. Click the ‘+’ button in the bottom left corner of the screen, then select ‘Create Aggregate Device’. Select the tickbox next to only the Scarlett 6i6.
Now, in Cubase, go to Devices > Device Setup. Click ‘VST Audio System’ on the left, then select your new Aggregate Device rather than the 6i6 (even though they’re essentially the same thing). Now test again - has that fixed the problem?
Jack // Focusrite Technical Support