This is kind of bizarre

I had a mini version of this experience, but since I was applying at the Service Canada counter just next to immigration I just had to go back and ask the immigration officer to do his job! I guess, however, since your COPR was filled out (I hope), you at least had clear evidence that you'd landed.
My advice would be to try and link your application (if you have not done it already), then give the IRCC a call in maybe about a week. You can take the opportunity to double check your address as well as ask whether there are any issues with your submission (for example the photographs). In my case the photos were okay, but they had my address wrong.
I think nothing stops you from getting your photos early, if you have doubts about them), but you can't send them yet anyway. What I would suggest instead is to take a ruler and check whether you've met all the photo guidelines (centering, size of photo, size of face, etc). If all looks good, then I guess chances are good that you don't need to resubmit photos.
All the best!