Sorry for the delayed response here.
OK I see. It looks like you set up RAID on this system and it looks like bootupd doesn’t handle this appropriately. There is an existing open issue against bootupd at Support updating multiple EFIs in mirrored setups · Issue #132 · coreos/bootupd · GitHub. Can you also open an issue for this against GitHub - coreos/fedora-coreos-tracker: Issue tracker for Fedora CoreOS so we can document the incompatibility and track a fix and possibly document workarounds there.