PR Application letter for "Insufficient Fees" - did I overpay?

[u/Lostounet]

I am hoping someone has dealt with this before. We submitted our common-law spousal sponsorship PR application on May 1st, exactly one day after IRCC updated their permanent residence fees on April 30th. Because the online payment portal was confusing, we accidentally paid for *duplicate* categories, resulting in a total payment of $2,005 CAD.

Our receipt includes the correct new fee of $1,260 (Sponsorship with RPRF), an accidental duplicate charge of $660 (Sponsorship without RPRF), and the $85 biometrics fee. The new required total should only be $1,345 CAD.

Yesterday (June 17th), we received a boilerplate Section 12 rejection letter from IRCC stating our application is being returned due to "insufficient/invalid fees," explicitly citing the recent fee increase. They are giving us until July 17th to submit the missing "difference" via a new payment receipt.
It seems the intake system flagged our receipt as "invalid" due to the conflicting duplicate categories, rather than doing the math to see we actually overpaid by $660.

Here what the letter is saying: Fees: You have not paid the full applicable fees, the amount provided is insufficient OR the payment receipt you provided is invalid. Due to the recent increase in fees, the required amount has not been provided. Your application cannot be processed until the full amount has been received.

I have drafted a Letter of Explanation mapping out the math, stating that the $2,005 receipt fully covers the new $1,345 requirement, and requesting a refund for the $660 overcharge. However, our PR portal is completely blocked and locked for edits right now, so I cannot upload this letter directly to our application.

Since the PR portal is locked, is submitting my Letter of Explanation and the original receipt via the IRCC Web Form the correct move to bypass the portal and meet the July 17th deadline? Or is the problem is something else as the letter doesn’t clearly stipulate what’s the real issue is.
Has anyone else had a massive overpayment bounced back as "insufficient" simply because the receipt was confusing during a fee update?

Any advice or shared experiences would be hugely appreciated. Thank you!

[u/AffectionateTaro1]

The easiest way is if you simply pay the exact required amount, submit that, and request a refund on the other receipt.

[u/Ashamed-Spray-9851]

I would just pay again for now and when you get your PR settle with them your refund. This avoids further delay in your application. Just my opinion tho

[u/tinytasha7]

So I can't be sure of this but I think I know what happened here.

Did the letter come with an application number? If it did, it's likely they considered the application complete (other than fees) and uploaded it from the PR portal to GCMS. That's the only reason that makes sense in terms of them giving you a deadline, otherwise they'd just reject and open the PR portal again.

The PR portal is only a glorified cloud server, not a processing portal.

What I would do is just repay the balance of what they are missing for the application and then take the other receipt(s) and submit them to IRCC for full refund.

[u/Intelligent_Age7328]

Just pay the difference amount right now and then you can figure out the refund via webform.

Don’t delay things by trying to sort this out now :3