Is he wrong though? If you went to a shop and spent $2,000 but forgot to pay for 3 items (say worth $5) by accident, I do not think the shop manager should be upset, or that you should feel bad about it? If it was a smaller/non-chain store, it would probably be free! If anything, the main annoyance is probably their stock numbers being out of date.
Making mistakes is human, and I do not think they should feel bad for what they have done (and for not correcting it), and this is coming from someone who cannot steal the bags that now cost 20 pence at Tesco and even went to buy imaginary food at Waitrose after I forgot to pay another time...