All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
It is most likely that the worker would not give permission to your father except with regard to something that he is authorized to give permission for, or perhaps he would pay on behalf of your father voluntarily. Therefore, you should not dwell on this subject because it opens the door to satanic whisperings. The matter is not serious, because the worker gave him permission to take the cup of coffee, and he acts as an agent of his employer; his action should be interpreted as valid and authorized, especially since the price of the cup of coffee is mostly insignificant. If you wish to adhere to caution and clear your father’s liability, then pay the price to the store, and you are not required to inform your father of that.
Allah Knows best.