Early in the film, Jaylah shows how she keeps the USS Franklin from being seen by Krall and his men, using a sort of holographic projection system.

But

>! Krall arrived on the planet in the USS Franklin.

So why did he seem ignorant of the vessel's existence? If he was aware, and didn't consider it a threat, why did Jaylah bother hiding it?  At the very least, wouldn't he have noticed that one day the vessel disappeared, to be replaced by a large rock, and gone investigating?