I am not sure why, but I have 2 products that now show “out of stock” on the category and shop page but when you click Selecto OPtions to go to the single product page, all variations are “in stock” and do not show the out of stock label.
Product has the out of stock class http://prntscr.com/nwvpep that’s why label appears. Enable the default WooCommerce theme Storefront and check if you have that class for that product when default theme is enabled. We’ll be able to help you only if that class does not appear with the default theme. In another case, you need to contact WooCommerce support.