This happens when the app is using some kind of keyboard extension. (not sure if there's a proper term for it)
For example:
In Safari, it's the search bar (for searching the current page) that causes it to happen.
In iA Writer, the extra set of keys causes it to appear. (annoyingly, the keys are still full size, even in the split view)
Same thing happens in Jump Desktop for the extra row of keys they added.
It only seems to be a "full split" when it's just a plain keyboard without any "extras".