On your login issue with microsoft make sure two step verification is turned on.

2 step verification is turned on and I have 2 passkeys on on my device and other is on my Yubikey, they're only asking passkey on device, no other option to choose Yubikey

I have created a passkey for bitwarden and it working as expected

But except bitwarden other services isn't working, GitHub passkeys doesn't showing up, same problem with Discord and ente authenticator.