It's in Film, TV, books: Mean Girls (2x), Never Have I Ever (2x), 30 Rock, Speak
The Nowhere Girls, Worm . . . just from a quick googling. there's a related "go to the bathroom to cry / be alone / be sad" seen of which this is one manifestation. It shows up a lot — but mainly in chicklit / girl movies apparently. 30 Rock it's not a scene but something spoken about.
also apparently some kind of japanese thing —
WikipediaToilet meal (Japanese: 便所飯, benjo-meshi) is a Japanese slang term and social phenomenon referring to the act of an individual eating a meal in a toilet room. In modern Japan, some people eat alone in a bathroom for various reasons; the most common reason is that they do not wish to be seen...
https://en.wikipedia.org/wiki/Toilet_meal