When somethings unavailable at restaurant

How do you guys handle it when a restaurant is out of a certain item? Can customer actually substitute something if I actually within the app click unavailable, contact the customer, etc., after the order is otherwise completed at restaurant and the bag is sealed? Tbh I’ve only done that a few times. Other than that, I just basically called and let the customer know but then I get messages from support that customers had missing items. I hate the thought of having to wait even longer there. What is the actual correct process?