There’s conflicting information about how to sign these forms - the application portal says not to print and sign any form, but IMM5990 needs to be notarized and that is normally done manually. So far it seemed like it didn’t matter how it was notarized (digitally vs manually), as long as it was notarized.Initially I signed them both digitally. but before they returned the app, I discovered online information stating that the IMM5990 form should be signed manually. On 12/12/2023, my common-law partner signed the form in front of a commissioner of oath, and I promptly submitted the updated document through the webform. that didn't work I guess
In your case I would call IRCC so they can better explain what the issue was. It wouldn’t make any sense to 1) say that you must sign everything digitally, then 2) return your application because you did exactly as they said. It also seems unusual that they’d return the application to you after asking for biometrics and everything. Hopefully it was a mistake!
Best of luck!!