A bodega is often (and usually unavoidably) more expensive than a bigger grocery retail chain that's further away.
Price conscious buyers will opt to drive to the bigger, farther away store because it has more variety, and the essentials are cheaper.
I know I do this.
There's a full supermarket a 10 minute walk from me because it's a dense area.
Everybody does this, unless its 10pm on Saturday and you are thankfully kissing the hand of bodega owner for being open at such absurd hour
Part of this is defacto deregulation allowing suppliers to overcharge smaller stores with less purchasing power than big chains. (The policy not to enforce https://en.wikipedia.org/wiki/Robinson%E2%80%93Patman_Act).
Part of this is overregulation, with zoning and planning departments enacting policies that make smaller retail spaces less attractive to builders and owners, leading to a low supply, and allowing egregious rent for well located small retail.
Yes, economies of scale likely mean that larger businesses can afford lower prices, but smaller businesses also get to avoid some costs (no large administrative corporate departments necessary for a one-location bodega), so the prices probably don't need to be as far apart as they are.