I have had a few transactions show up in both Paypal and Stripe that look great on the merchant side, but the order number associated with them is from an older order that the customer placed. For example, I had a customer place an order today and the transaction came through just, but has an order number assigned to it from 3 months ago. This makes magento not create a new order because the order number already exists. I am not sure where to start looking to find the issue. Any help would be greatly appreciated.
Turns out the issue was PayPal Express Payment not correctly updating the magento quote table. Some of the quotes still had the "is_active" table still set to 1 after the order was placed. This issue only showed up as long as we were using the PayPal Express Payment Method. We switched to Stripe Payments and no longer have the issue.