Can you check which Firmware is on the Yubikey? newer Yubikeys come with newer Firmware which creates some headache as older Yubikey 5's are essentially having CTAP2.0, while newer ones have 2.1 or other changes which affects some things in regards to Resident Credentials, like CTAP2.1 and 2.1PRE have the ability to manage them individually rather than the CDRW approach of nuking everything once the 25 are full.
Is there a specific failure Message? one plausible reason could also be that it is plain full as the Yubico devices have one of the Lowest amounts of Resident Credentials you can store.
Generally new things at the WebAuthn layer should not affect the CTAP Layer in a meaningful way as WebAuthn is basically the method on how a relying Party's Website has to communicate with a Browser and how the Backend verification works but how the Browser communicates with any given Authenticators is iirc handled elsewhere, like for FIDO2-Authenticators like the Yubikey, CTAP is used, while the transport with phones uses its own protocol iirc.
Regards
My1