A lot of these list maintainers put a lot of work into not breaking things, but their are just too many websites out their to know if a block breaks one of them or not. Send the list maintainer an email - or if they are on Github/Gitlab open a ticket and have a discussion. I think you'll find many of them are happy to remove breaking domains. Of course whitelist is always an option too if the list maintainer disagrees with the removal of a domain.
Also, there is a popular whitelist project for the Pi-Hole that can make it more user friendly: https://github.com/anudeepND/whitelist