People are often surprised to hear that when one uses or consumes an item after discovering a defect or discrepancy he is often deemed to have been mochel the discrepancy and has waived his right to make a claim or return the item. There are many variables that affect this Halacha such as the manner in which multiple items are bundled or sold together, the type of discrepancy, the nature of the buyer, the circumstances in which the buyer proceeded to use or consume the item, the residual value of the item to the owner if returned, and many other variables that can completely change the outcome of these cases.
Therefore, if you ate the dish and then called to complain it is entirely possible that you have been mochel the discrepancy and lose the ability to have a claim (it is not entirely clear that there is a monetary claim in the first place/ it may be like בשר איל מסורס in סימן רלג). Even if you called before consuming the dish, the amount of the claim- if any- would likely be lower than the refund you received.
Complicating matters is the fact that Grubhub acts as the agent of the restaurant, transferring all funds less commissions to the restaurant. As per its service terms it does appear to have the right to deduct refunds and discounts granted to customers from the funds it transfers to the restaurant (it’s unclear who gets to determine when a discount or refund is appropriate- Grubhub or the restaurant). It would still appear that any refund claim is really being lodged against the Jewish restaurant rather than Grubhub itself. This would seem to be similar to doing a chargeback through the credit card company against a Jewish merchant.
The best would be if you can get the owner/ manager to agree to the refund as a goodwill gesture; otherwise consult a Rav who is well versed in choshen mishpat for your specific situation for guidance.