Initially. It should be said that WooCommerce is considered a plugin and therefore your question could probably be flagged as ‘Off-topic’. This (however) is such a bullshit and self-deprecating for this StackExchange, so I’ll answer it anyway. 🙂
But next time you have a WooCommerce-question, you should ask it on StackOverflow (apparantly).
My first thought is that you could have ‘Backorders’ enabled on your variations. Either that or that you have stock enabled on either the variation-level and/or your product, and that somehow makes it possible for customers to buy something that is out of stock.
If this isn’t the answer, then perhaps try to add a screenshot of one of the problematic variations and also the ‘Inventory’-tab of the product.
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