This can happen in very rare, coincidental cases within a very specific, narrow window of time; unfortunately, the only solution is worse than the problem itself.
For products that Limit Available Stock, our system adjusts the quantity remaining in stock whenever we process an order for that product after payment is completed. However, it may be possible for two buyers at the same time to add a quantity to their respective carts which can each be met with your available inventory separately -- e.g., if you have 1 unit left of an item, multiple buyers can have qty=1 of that item in their cart at the same time, up until one of them completes a checkout payment to actually purchase that item. Thus, if the first buyer proceeds to checkout, and then the second buyer also takes their order to checkout before the first buyer's checkout payment is completed, both orders will be processed, resulting in a negative quantity remaining in stock.
We do try to catch the majority of these cases by rechecking available inventory every time a buyer's cart is shown, so if a completed checkout alters your inventory in a way that affects a buyer's in-cart quantity while they are still browsing your site, their order quantity will automatically be adjusted to match available inventory the next time they view their cart before checkout. The only more foolproof way around this would be if we adjusted available stock based on what quantity buyers have merely added to their cart even before they go to checkout, but that would simply tie up all your available inventory in pending cart orders which may never proceed to or complete checkout at all.
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