Same also happened to me this morning, completed a Steel Path full experience run while deliberately grabbing any Koznik I could to build Sun & Moon. Extracted and got none of it, nor any of the other open world resources as far as I can tell. Oddly enough the clamps for completing, as well as a random fish from maw fishing, were retained properly.
Ended up having to rerun for the Koznik then just quit out after a random decree, that saved my resources.
EDIT: While I remember, it was Fear spiral I completed, but Joy appeared on mission complete screen. Don't know if it's something to do with Spirals changing while in mission due to how long they take.