This is a small quirk of Japanese shopping culture. In Japan you don’t hand your money to the cashier. If you try to, some will look at you funny while others will take the money but feel a little insulted.
At every register there is a small tray with a rubber bottom. The cashier will usually slide this in front of you after telling you the total for your purchase. You put your money in the tray, which the cashier then takes, counts, and puts in the register. Any change is then put in the tray which you, of course, will take.
If you forget your change in the tray you can often expect the cashier to call after or even chase you as you leave the store. Even for amounts as small as five yen.