"It was very blackened, as if it had been charred," she said.
I don't think there's any way the body could have been charred during the flight. There's nothing in the wheel well that could burn a body -- as the article mentions, a person is a lot more likely to be frozen traveling at altitude. If the body was burned, it would have had to have been foul play, like someone killed the man and stuffed his corpse into the wheel well.
Maybe it was just grease and dirt from the landing gear.