Do you have this problem when parent theme is enabled or with child theme only? Do you have the problem when Storefront theme (default WC theme) is enabled? Try to disable all 3-rd party plugins and check if the problem will be solved.
WC plugin has added the new option to adjust the number of products per row http://prntscr.com/idnyzh and you need to be sure that you set the correct number of products there.
Also, you had fixed height for the column in custom CSS. It caused additional problems. And this code with changed width for the global columns http://prntscr.com/idohmo is not a good practice.
So, check the shop page now and let me know what problems do you still have?