Hi there,
As far as I know if you've followed the checklists and the online guides, you should be ok.
Example: We sent 2 statutory declarations of common law union, 1 for the OWP application and 1 for the sponsorship (not mandatory, but we sent it anyway as we'd rather err on the side of caution).
So if there's any mandatory documents on both checklists, then you should've sent 2 separate copies, one for each application.
If that's not what you did, then you may have issues as technically your application is incomplete. I'm not sure how you can rectify this, but I'd give the IRCC client support a call and wait for other replies from more experienced members.
Good luck!