We are seeing this problem sporadically with customers like yourself that have updated from a previous Mac OS X version to 10.11. Apple removed Kernel functions that affected more than just our products. Any software that relied on kernel operations is most likely causing the problem and needs to be removed from your system.
This issue stems from some older software on your system that is not compatible with 10.11 that is causing the Core Audio Driver to reset, when it does, the iTwo (or any USB Audio interface) will fall of the bus, when the bus resets, the audio comes back (then the process repeats).
This is not a Presonus problem as Presonus does not make the device driver for OS X, this is an apple product. We have notified apple of the issue so they are aware of it. You may want to contact Apple.
You'll need to check with all the companies that you have 3rd party software installed for to make sure their applications support El Capitan. Some companies still do not recommend upgrading to 10.11 as not everyone has updates for it yet.
To find the offending process or application that is crashing the audio bus, open up your System Report, and scroll down to Logs under Hardware in the left column, and look at the Apple System Log to see what applications are failing. You might get lucky and find the offending application. If this takes too much time you may want to consider a reinstall of your OS.
I don't mean going back to 10.10 and upgrading again, I mean use Disk Utility to create a new disk partition and Install El Capitan fresh (takes about 30 minutes). If you do this problem will not occur. You will need to reinstall all your software however you'll be getting the latest versions that work with 10.11.