This is a known bug; work-around is to add id.me to the “Excluded Domains” list (under Settings > Notifications).
I’m not sure exactly what is going on in your setup, but I will not that I can successfully use Yubikeys as 2FA for my id.me account. Under Sign In & Security > Security, note that they offer two distinct options: “Passkey” or “Security Key”. If you previously tried to register a passkey using the “Passkey” option, perhaps you can try it using the “Security Key” option (and see if Bitwarden intercepts that request).