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?
Edison has been stuck on the planet for a hundred years. By the time of his last recording, he already seems to have been mentally and physically affected by the life extending magic. I mean dues ex machina. Only 3 crew members have survived, and it's was shown that Krall has attacked and taken passing star ships and their crews to use as fuel for extending his life. The Franklin was a derelict, a crashed and useless ship to him, and his building hatred for the peace mongering Federation that left him to die would have made him give up a daily reminder of the UFP for the mining base and it's advanced technologies.
He has been blinded by rage and his mind tampered with by a century of absorbing alien life force that has physically changed him. He simply didn't notice or care because he was locked into his one track mind, courtesy of his military oriented mindset.
Same reason they didn't hunt Jaylah down relentlessly. It just wasn't a threat to Krall. His 2nd in command had to practically beg him to get permission to chase after Jaylah when the scoobies attacked the base.
The reason she hides the ship is more likely for hiding from random patrols or other people that crashed on the planet, like the scavengers she had to fight off to save Montgomery Scotty.
