In an online concierge system, a shopper retrieves items specified in an order by a customer from a retail location. The online concierge system optimizes order fulfillment by selecting a retail location for an order that is most time-efficient and that is most likely to have each of the item in the order available. Hence, the online concierge system may select a less convenient retail location that is more likely to have each item being ordered available. To predict whether a retail location incompletely fulfill the order if selected to fulfill the order, the online concierge system trains a machine learning model based on prior orders fulfilled by the retail location, a shopper retrieving items in the order, items in the order, and other features.