The top pick goes to WooCommerce, although an open source E-commerce solution on top of Wordpress, it has some terrible decisions under the hood.
The top pick would go to mixing presentational logic with business logic. For example, to render a table, instead of exposing an array of objects to allow the developer to loop through it as he/she sees fit, WooCommerce will force you to use a PHP function that renders a table for you and there's actually no way to modify the presentation logic if you wanted to.
It's a really fundamental programming paradigm that even top open source companies fail to adhere to.
Again, I'm not saying this to attack them or the maintainers behind the code, just my opinion of why I think it's bad quality code while respecting the fact that developers still do take time and effort for us to enjoy something with freedom and zero cost.