>>85789126The Crystal Gems don't need to eat, so one of the guidelines for storyboarding episodes is that the gems, sans Amethyst and Steven, shouldn't be shown having a snack in the background or something. The joke was just one of the storyboarders making an inside joke by going "look, Garnet clearly ISN'T eating the popcorn in this scene, so it's alright".
It's similar to the joke about Garnet not being able to ask questions in the other episode.