I can't see them having any "liability" for not releasing the lower after the 3 day waiting period expired. I am sure the Protection of Lawful Commerce in Arms Act would protect them. I don't agree with FFLs choosing not to complete transfers after the waiting period, as it allows the government to prevent lawful gun sales by simply delaying and the 3 day provision is essential to keeping the NICS system from becoming a backdoor gun ban through delays. That said, I can understand a store deciding not to transfer to someone who hadn't gotten a clean NICS result, but they shouldn't be charging a fee for those who don't want to wait 30 days.
Maybe Troop L told them this.