But I don’t think they’re overshooting per se. I think they’re landing the centers in the right place, but the outer pieces account for most of the moment of inertia, and they’re flexible, so the overall assembly is deforming. Deriving the optimal control law for that could be a bit messy. I would guess that it involves bringing the center piece nearly to a stop slightly short of 90 degrees and then gently bringing it the rest of the way.
[1] https://build-its-inprogress.blogspot.com/2017/12/controls-r...
Even in simple linear systems with a PID, a bit of overshoot may improve the response time. It's not always desirable but in this case there is no problem with it. I also liked the other commenters idea that perhaps the parts of the cube are moving further than the centers and then falling back in place.
Though I suspect the thing might fly apart if timed wrong. That’d be worth watching.