I’m not sure if anyone else has had this issue, but in Chapter 17 (Wind Crystals in Labyrinthos), it wasn’t following the prescribed grid and flying up and out to the gathering spot, but flying straight into a stone building next to the Aetheryte.
It took me a few minutes, but I figured out it was because the preset for the crystal gathering was saved to attach to a different grid from the one the chapter was meant to be following. A quick overwrite of the Crystals preset fixed that.
So, if you’re having this issue with any of the chapters double-check which grid the current chapter’s preset is attached to. It may need an overwrite to the correct one. I hope this helps someone. ^_^