Update: Home office replied - "Please note that although you have received this warning message, you should be able to continue with the completion of the form if you have the correct COS number. You can continue with your application and complete."

Yeah, I applied as well. Will carry the doc with me for the visa appointment. Good luck!

were you able to resolve this issue? if yes, what did you do ?

I am having the same issue. However, I read in another thread that submitting the pdf and screenshot of the assigned status should be more than enough.
I have also sent a mail now ApplyOnlineE-Support@homeoffice.gsi.gov.uk as suggested in that thread.
So let's see!