Didn’t check with other 3dNPC companions, but I have found myself alone in some cave or dungeon, while Zora’s standing outside waiting for me. I tried fast travelling, running around to better position an the cave entrance, nothing works. She follows me to the entrance but does not enter with me.
Last thing I was struggling with was Wolfskull cave (Potema questline). Had to reload an earlier save and go recruit Lydia, because my difficulty and playstyle doesn’t allow me to finish it alone.
I also have an AFT patch whic doesn’t seem to be working, i.e. recruiting any 3dNPC will disband another one. Didn’t check out with more than 1 vanilla followers. But anyway, I doubt it has something to do with the (?)pathing issue.