Are there any real world examples of Kings punishing their lords for failing to protect the commonfolk? Was this rare?

Depends on how you view the expansion of royal justice, which could involve royal judges and sherrifs pursuing criminal charges against noblemen for acts of violence including against smallfolk. And certainly when you get to the Late Middle Ages and you have royal attempts to restrain bastard feudalism, it becomes more common.

But earlier on, in the Raoul of Cambrai era, the kings lacked the capability to prevent private vendettas from harming the commonfolk.