notatliia
As I understand it, you are trying to sign in to Proton with a Yubikey over NFC. That should work fine, but you need to install Google Play Services for practically most Yubikey functionality to work (Android (AOSP) does not have native security key support).
However, most of the Proton apps don't support signing in with security keys. Last time I checked, only Proton Pass supported this. But their websites do support it.
notatliia Installed yubikey app
Do you mean the Yubico Authenticator app? Or some other app? As far as I know, you need Yubico Authenticator for OTP support with a Yubikey – at least it seems to be what Yubico recommend.
TOTP should work just fine on GrapheneOS. Not clear to me what issue you are experiencing.