An employee of a jewish-owned store undercharged me a small amount (a quarter, etc.). When I brought it to his attention he told me not to worry about paying it.
Does he have the ability to do this?
The issue here is if we can assume that the owner would not mind that the worker forgave some of the payment, especially due to the fact that the amount is very small. If it was a worker with a level of authority, then you don’t have to worry about it, however if it was just someone who stocks the shelves and he was too lazy to deal with it then it should be returned to the store. Alternatively, you can call the store and ask for the manager and ask him, and if he says that it is alright then it is fine.