I've occasionally gotten those emails. I think sometimes there's a hiccup where the credit card company rejects a charge for some reason (probably some fraud detection algorithm) but then OMNY tries it again and it goes through.

On the reimbursement front, for several months I was submitting credit card statements to Wageworks/Healthequity to get reimbursed for my transit benefits, since you couldn't add a Wageworks/Healthequity debit card to ApplePay. But they finally enabled ApplePay for their cards a few months ago so now I just use that. I'm missing out on some Chase points, but those points aren't anywhere near worth the hassle of redacting credit card statements every month to send in.