Perhaps a Trainer released a few, then they began to breed. Eventually, there would be many fossil Pokemon as a result of the original pair.
They could have gone extinct in the first place because the climates in which they lived changed. Perhaps the climate in the Crown Tundra is more suitable than other places, allowing fossil Pokemon to survive in the wild.
This is purely speculation, as there is no real reason. It could just be Game Freak doing what they want, with no reason whatsoever.
Hope I helped!