This is explained in the original script and the novelisation;
It was a pretty unusual star system to begin with. Ceti Alpha V and Ceti Alpha VI rotate around each other in a shared orbit. Some instability would be expected.
The shock of Ceti Alpha VI exploding moved the main planet out of alignment so the charts would be inaccurate in any case (see below)
In order to prevent Khan from being released, the planetary charts were deliberately erased.
KHAN: This is Ceti Alpha V ! Ceti Alpha VI exploded six months after we
were left here. The shock shifted the orbit of this planet and
everything was laid waste. Admiral Kirk never bothered to check on
our progress. It was only the fact of my genetically engineered
intellect that enabled us to survive!
On earth, two hundred years ago, I was a prince, with power over
millions -- now, like Prometheus I have been left by Admiral Kirk to
digest my own entrails. - Movie Script
"You lie!" Chekov shouted. "I saw the world we left you on! It was beautiful; it was like a garden—flowers, fruit trees, streams … and its moon!" Chekov remembered the moon most clearly, an enormous silver globe hanging over the land, ten times the size of the moon on Earth, for Captain Kirk had left Khan and his followers on one of a pair of worlds, a twin system in which planet and satellite were of a size. But one was living, the other lifeless.
"Yes," Khan said, in a rough whisper. "Alpha Ceti V was that, for a while."
Chekov gasped. "Alpha Ceti V !" The name came back, and all the pieces fell into place: no official records, for fear Khan Singh would free himself again; the discrepancies between the probe records and the data Reliant collected. Now, too late, Chekov understood why he had lived the last few days under an increasing pall of dread. - Star Trek II: The Official Novelisation