Some caves are blocked by massives doors. And doors need keys.
With the help of your abilities, notably the possession one, you'll be able to find strange cubes. That's the keystones you're looking after!
Sometimes really well hidden in the darkest parts of the many underground chambers, or in plain sight in inaccessible parts, you'll need your abilities to get them.
Those puzzles make you use the different strengths of each creature in their environment, allowing you to progress further.