Ninjas are assassins, not frontline troops. One at a time, sneaking up on a hero, when they can use stealth to their advantage, they can do far much more good (or evil, as the case may be).
Or: The Dragon or Big Bad will send out his worst mooks en masse as cannon fodder, hoping that quantity will make up for (lack of) quality, while his less common, more competent mooks get sent out in smaller groups so to make better use the scarcer resource they represent.
Or, the massive army of mooks is really just one enemy with Doppleganger Spin powers. As the clones are mowed down, the rest become stronger.
The hero is a mage with spells to cut down weak mooks en masse who was never meant to solo strong lone enemies.
An army of good footsoldiers takes on a lone badass villain.
Alternatively: The more zombies show up, the more powerful each individual zombie seems to be.
The hero jumps into a group of enemies, only to find out that they are a lot more powerful than they look.
Zig Zagged: Various groups of enemies give the hero different levels of trouble with regard to defeating them.
Averted: The hero knows better than to recklessly attack his enemies and brings plenty of allies to help him out.
Enforced: "We need the hero to fight off hordes of enemies so it'll look really epic."
Lampshaded: "Who knew one guy could be so powerful?"
Invoked: The hero begins drawing plans for attacking the enemy fort, one of them being to charge wildly at the opponents and hope for the best.
Exploited: The Big Bad sends out an army of his weakest mooks in order to get rid of deadweight while keeping the more Elite Mooks to fight the heroes in one-on-one battles, knowing they are more dangerous.
Defied: The hero charges into battle, thinks about it for a second and turns back to get reinforcements.
Discussed: "Hell yeah, they brought out the ninja! Those guys don't stand a chance now!"
Conversed: "You ever wonder why one guy is capable of taking down entire armies of henchmen with such little effort?"
A single hero charges into the group, expecting to defeat his enemies easily. Turns out this was a pretty bad idea as the opponents gang up on him and finish him off.
Or he does beat them all... but because there were no witnesses, no one will believe that he has done such a thing.
The reason why the hero was able to take down a large group of enemies with such ease, was because all of them were exhausted, injured and taken by surprise. Trying out the same feat with a properly prepared group would be suicidal... But the hero does so anyway due to Suicidal Overconfidence.
...But the challenge of taking on so many enemies at once forces him to fight with even more strength, since he's now fighting for his own survival.