I think it started from 9/21 version and still happens in latest version.
So I chose to help Coockie and follow her to the portal. During the cutscene when Cookie was talking she walked all over the place like some random NPC did. And after I defeated the Oger both Magic spirit and Cookie ended up in strange places.
But after I left and teleport back everything went back to normal. The rest of the plot is also normal.