In Japanese schools, typically they have set of outdoor street shoes and indoor shoes called "Uwabaki." Inside, there are typically individual shelves or lockers for everyone's shoes. These shelves/lockers will occasionally have a space for students to put and swap their outdoor shoes for their indoor shoes. This is typically done to keep the floor from being marred by outside elements and maintain its polish for a longer period of time.
The general idea (depicted in anime and manga) of bullying is to either steal them (and toss them away or place them in an inconvenient place) or fill them with tacks or garbage (sometimes also defacing them). The purpose is usually humiliate them and/or cause them distress without actual confrontation. The sandals she wears are probably her indoor shoes, and the idea is probably to take enjoyment in humiliating her by making her walk home without shoes or in her indoor shoes. In essence, the idea of this is to shame the bullied victim (who typically react passively), who loses dignity/"face", which elevates the ego/status of the bully or bullies.