Everyone is right. You should have went back once you were unsure whether or not you had been charged correctly. Look at it this way, the guy would probably help you and anyone else who comes into the shop as good as he can, which is shown by him selling you more than he was supposed to anyway. Seems like a nice fella to me. Then you don't have the integrity to go back and ask if he made a mistake and if you owe him for the cigars?
He did a very nice thing for you, the least you could do is make sure he won't get in trouble for helping you out. That's just my humble opinion on this matter.