It took me a few hours, to debug the cause of an out of stock error for a Woocommerce site.
The product variation had stock available. When performing a checkout it cause an error that the product didn't have enough stock.
I finally figured out what causes this problem:
Woocommerce tries to reserve a product via the function
'reserve_stock_for_product' (woocommerce/src/Checkout/Helpers/ReserveStock.php)
This method joins several tables: wp_wc_reserved_stock and wp_post_meta.
In my case the tables had different storage engines. wc_reserved_stock had a INNODB storage engine. wp_post_meta was MyISAM.
This fails with this particular INSERT query. Because it cannot joins these tables in a single transaction.
So don't mix table engines!!
(Which happen when you migrate an old site to a new server with a different default storage enginge)