Quote Originally Posted by Mercen-X
The Cetra were migraters . . . (SPOILER)some of them got lazy and they stopped moving just before the "Calamity from the Skies" came and that's why that crater never got repaired. Jenova ended up infected nearly all wildlife and made the moogle extinct.
(SPOILER)The game never says anything about Moogles becoming extinct due to JENOVA, nor is it implied that there ever were Moogles in that world outside of the Gold Saucer's games and attractions.

By the way, some of the Cetra giving up their journey had no bearing on the Northern Crater not being healed. Ifalna even says that the Cetra who did try to help the Planet guide its Spirit Energy had to give up and let the Planet do it on its own due to the severity of the wound. Further still, the Planet even told the Cetra to leave that area just before JENOVA approached them, though the warning came too late. The Planet had to do that on its own.

The wound hadn't yet healed because it's a big ass wound. Further still, Ifalna seemed to believe that the Planet would never be fully healed so long as JENOVA remains.