Not Available in this Split View Mac El Capitan
When you get the seeming error "Not Available in this Split View" that means that those windows are not available in the split view and I couldn't understand why. Here is why: they're too big to take up only half the screen. I was trying to open two OmniFocus windows in split view and I did it at first, but then, they popped out of split view and i couldn't get them back.
The reason was that I had opened the side bars and inspector so it made the content too wide to be available in split view. If you're having trouble with this, try to hide some horizontal window content. It may be that your app just has too much going on to ever be in split view mode, though.