Discussed and averted in An Entry with a Bang!. It takes a lot of Clancy-Earth planes working together to bring down one BattleTech aerospace fighter, and that's only because they were fighting separately. The analysts realise that against a proper House or Comstar ASF unit trained to fight together, C-Earth will be in big trouble.
Played and lampshaded over and over again in Uninvited Guests, not only with actual ninjas, but with the Espada.
Averted in A New Order by the Dark Kingdom. When the senshi start getting more competent they send multiple youma at once, which makes the battles harder.
Done almost literally in Eroninja. Nagato, using more efficient chakra receivers and a mind-controlled Shukaku, invades Konoha with 200 Paths of Pain. However, despite having the chakra to power them all, the bodies are lower quality and Nagato can only split his attention so many ways. So instead of six invaders each easily kage level, it becomes more a battalion of elite jounin.
The Dashverse: The Mane Six have a much easier time fighting the amassed forces of Sombra's minions once they're stormed his castle than they did fighting the smaller groups they'd encountered on the way there.
In a Digimon fan fiction Zero 2 A Revision, Umbradevimon and Demon have both invaded the Real World at the same time and ended up competing with each other for dominance. While the former uses as many as 1 million Black Gear controlled Digimon of various levels, the latter uses 10,000 well-trained Bakemon along with his Black Generals Ladydevimon, Deathmon, Marinedevimon, and Colonel Soulmon aided by his own Archfiend Castle and the Typhoon of Flame. By the time Demon managed to repel Umbradevimon from the Real World, their forces dwindled down approximately the same amount as each other which means Demon easily won against Umbradevimon.
White Devil of the Moon has the fight in Beryl's throne room, where a just-kidnapped Miyuki Takamachi takes on the assembled youma there (which are legitimately dangerous and cannot be permanently harmed without magic) and, due to her own fighting skill and the monsters getting into each others' way, manages to actually cut Beryl once before being overwhelmed. Double points for Miyuki being in fact a descendant of a ninja clan herself.