What may have happened depends on for which airline the commuting FA worked.
If she was UAL mainline, she has to list for F to be seated in F. If you list for F, but don't clear into F, you can be seated in a lower cabin. If you list for Y that's all you can be seating in. Being seated in a higher cabin requires payment of a fee. For UAL employees, it can either be paid up front, and refunded if you don't clear, or payroll deducted after the flight. For that reason, when I commute, I always list in F.
If she was a UX employee, they must pre-pay when their list for the higher cabin. They don't have the option for payroll deduction.
If she was an employee of some other airline who was jumpseating, I'm not sure how that works. A pilot jumpseater can be put in an open F seat if Y is full but I don't know if that applies to offline FA jumpseaters. In either case, no charge would be due.
If she was an employee of another airline traveling on a ZED pass, those are only for a the cabin for which they are purchased and F ZED passes are not always available. This is the least likely, though, as a commuting offline FA would just jumpseat instead of buying a ZED pass in most circumstances.
The key would be for her to understand the rules, as they applied to her, before hand so that she'd be prepared. There just isn't time to figure it all out while the agent is trying to get the door closed and the flight out. Just like casual flyers, if you don't non-rev a lot the details can be pretty confusing.