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?