I've been denied miles in the past for using a discount code I found online while still purchasing from the Mileage Plan shopping link. I believe they don't allow discounts or deviation from the standard link they've provided, and it looks like the Apple Govt store discount is technically a different "Apple Store" than the normal. Imagine someone/a computer is reviewing these to approve/deny miles, especially when it meets a higher threshold like this. If it had been a pair of Airpods, maybe they'd have just let it go.. You can keep trying, but you're probably not gonna get them to budge too much unless you can confirm you're within the terms/conditions.
FAQs: https://www.mileageplanshopping.com/faq____.htm
T&Cs: https://www.mileageplanshopping.com/terms____.htm