"Seems she was obeying the rules and they still stopped her. "
The plastic baggies are not meant for beverages, but for medical, hygenic, and cosmetic gels and liquids. If that were true, people would be slipping bottles of water, cans of coke, or containers of coffee inside those plastic bags to get them past security.
From the TSA:
"If you’re not traveling with a baby or toddler, any formula or breast milk you’re carrying must meet the requirements for carrying liquids, gels and aerosols (3-1-1)."