A good example might be the original death of the Hobogoblin in a Spider-Man/Wolverine special. Even though the character was supposed to have enhanced strength that made him able to go toe-to-toe with Spider-Man, he was still overpowered and killed by (IIRC) a group of ordinary henchmen.
This turned out to be the only plot hole that Hobgoblin creator Roger Stern needed to introduce a retcon that allowed the Hobgoblin to be REALLY revealed as the suspect that he'd originally intended (Stern had left the book before the ongoing mystery was resolved).
This turned out to be the only plot hole that Hobgoblin creator Roger Stern needed to introduce a retcon that allowed the Hobgoblin to be REALLY revealed as the suspect that he'd originally intended (Stern had left the book before the ongoing mystery was resolved).