Warning: Item level quantity will be ignored

Item level quantity will be ignored. The sum of the quantities for all the variations will be used for the listing quantity.

To resolve this warning that might also cause incorrect quantities for the variations, check if the "Send the product with variation" is enabled. Find the option in the Ebay Profile. Unchecking this option is useful only when there is 1 variation on the product and you want to create an eBay listing as a single product. If there are more variations on the product page, this option should be checked.