Tier 3 of It’s Not Over requires you to hit your opponent after the KO 30 times.
When you win a match, you'll enter a win pose. Press to regain control of your character. You can now hit your opponents body with attacks. Their hitbox is very low, so you'll have to use attacks that hit low enough. You get a little bit more time to score hits in Marvel Super Heroes. However, in Marvel vs Capcom, you're allowed to use hyper combos.
EVERY hit you do adds 1 to your challenge counter. So, in Marvel vs Capcom you can take advantage of this by choosing the right hyper, such as Wolverine's berserker barrage hyper and complete the challenge in just two to three rounds.