This problem is especially acute in chemistry on Wikidata, where chemical elements use "instance of chemical element" even though it has been established that chemical compounds should not use "instance of chemical compound" [
As we discussed many times, it's natural to model "chemical element" as "type of substance" or "type of atom" depending on the definintion you take. But no question elements are either subclass of substance of subclass of atom however. It's a natural case of metamodeling, similarly to the "car model" example. And no, using instance of has not be proven to be incorrect at all.