Because there are so very few craters. During the 4+ billion years we thing Pluto has been around, vastly more objects should have crashed into it.

If the surface is 100 million years or less, the number of craters makes sense.

Or we could have some other basic assumption wrong. Science has only known about this since this morning...

Craters, or lack thereof. They assume some rate of impacts, validate against other parts of the surface, other planets, and Chiron. No craters, the surface has been remodeled too recently for impacts to mark it.