This depends on the rules. In Chinese rules prisoners (i.e. tokens that you ate) are not worth any points, but all territory and stones of your colour are worth points.
In Japanese rules the prisoners are worth points, together with the territory. This makes it disadvantageous to capture some shapes even though they are dead (such as bulky five), so the rule with Japanese is that you don’t need to actually capture dead shapes at the game end.
Only after both players passed, and they dispute whether a group of stones is alive, the capturing will actually happen, but this does not affect the score. It only decides which stones are dead (and hence prisoners) and which stones are alive. The scoring will happen on the position after both players passed.
I was confused by this as well, see this topic.
And as Adam said, if you don’t understand this, don’t worry too much about it. For beginners it’s safer to play with Chinese rules, since they are easier to understand. Then you don’t need to worry about prisoners or dead shapes that shouldn’t be captured. 