@galaxis those instances have all been around a long time. They all existed before Mastodon implemented ActivityPub, as was the case with my instance.
I think that if there are follows that were made long time ago when Mastodon only used OStatus the subscriptions stayed on that protocol even when both instances involved got upgraded. You'd probably have to manually intervene to change them or wait for the other instances to upgrade to v3. I don't know of any other automated way...