Not IRCC fault. This is your wife fault. On the questionnaire, there was one question asked about country of residency. If she selected Canada, she didn’t have to pay for biometric. Biometric fee doesn’t include on my application fee and Right of Permanent. Go back to ur application and submit page and see if you made mistake for that one. Raise CSE with supporting documents such as bank statements or utilities bill to prove that you guys are in Canada
Good luck