@yasirhashmi15
1. How did you spouse get her passport request letter? Did you contact IRCC before this?
2. Did your spouse receive her COPR with her passport? As I understand, the visa office has to stamp a PR visa in the passport and send NOT signed COPR which will be validated/signed during the landing procedure.
I think if your spouse and you are getting portal credentials, IRCC assumes you both are inside Canada. It happens if you both have status (any kind of permits) in Canada. But the problem is people with status in Canada not always have a valid visa to enter Canada.