I normally fasten a few of the buttons/poppers of the duvet cover before loading it, this usually stops anything from getting inside the cover itself.
As for a large item tending to gather smaller items into a ball, I think this is something I used to see with old-fashioned machines decades ago, but any machine designed in the last 20 years will normally have clever tricks to minimise this sort of "bunching" by reversing the drum etc to even-out the load. My current machine (Bosch) will actually refuse to spin the wash if it determines that it can't be balanced. This only rarely happens with washing an actual duvet rather than just a cover.