Custom Stores Sharing Orders

I separate my orders into multiple custom stores depending on their source. Over the past couple weeks we have noticed two of the stores sharing orders. One of the two stores should not have any orders right now. I have checked the sql query that we use to get the orders for that store and it will not return any orders. The other store has new orders everyday. Some of those orders go into the right store, some go into the store that shouldn't have any orders. Assuming my sql query is correct, what is the next step in troubleshooting this problem?
Thanks.