This article is about something subtly different than overcharging: it's about consumers believing that they're paying one amount (the list/sticker price), and being charged a different amount (typically higher in the company's favor) at checkout.

In my experience, this doesn't really happen with bodegas: they might be overpriced in the "this is a bad deal for milk" sense, but they don't misrepresent their sticker prices to any degree that I've ever experienced.

(But also, I don't think bodegas do categorically overcharge in NYC. I think they're about the same as grocery stores, i.e. there's a large amount of internal variation in pricing because people generally don't want to make multiple bodega pit stops just to save $2.00 on eggs.)