Do you recall the exact phrasing of the clue? I’m not entirely convinced that “Wile E. Coyote” was the nemesis of the Roadrunner. There were a couple cartoons with Wile E. Coyote as a foil for Bugs Bunny, and he introduces himself as such in those cartoons. But I don’t recall that name ever being used in a cartoon with the Roadrunner. I seem to remember him being referred to just as “the Coyote”, and that character never spoke. I doubt even Jeopardy would make such a fine distinction, though.
There was also a third character, Ralph Wolf (the foil of Sam Sheepdog) who looked exactly the same except for a different colored nose.