In theory, cancelling a combo sounds like kind of a dumb idea. After all, in a fighting game, the more times you hit an opponent in sequence, the better, because you do more interrupted damage.
Whilst it's true that once you begin hitting an opponent they have very few options to stop getting hit, the longer your combo is in Injustice 2, the less damage you'll start to do until the combo has finished.
What this essentially means, is sometimes the flashier (pun intended) combos aren't always the most effective in terms of damage, and that sometimes it's better to stop hitting your opponent so you can reset your combo-counter and deal more damage in two separate attack chains, instead of one big one.
It does seem a little backwards that once you become good at the game you have to then almost be purposefully bad at it, but considering your opponent could Clash at any point to escape a combo or spend some meter to pull off a Block Escape, it does help to keep in mind that several short combos are a lot safer to pull off than a couple of long ones.