I personally don't have a problem with the missing Ceti Alpha V planet.
This was obviously a backwater star system that nobody cared about. There are billions of solar systems in the galaxy.
Only the astronomy section could care less if one of their charts is off. Planets probably disappear from their charts on occasion. Perhaps they chalk it up to a probe taking the initial readings of this section of space and not being 'entirely accurate'.
All Terell was interested in was finding a suitable planet not charting space. And you think why would Chekov not remember the significance of the Ceti Alpha system, since Khan knew him? Perhaps Chekov and the rest of the crew weren't told of Khan's exact location. Just that he'd been 'taken care of'. I'm sure after he'd tried to kill everyone, no-one was that concerned about his welfare.
I have more concern about the 72 torpedoes and maybe in 20 years I'll fangirl explain it but it doesn't make sense to me right now. IMO the writers needed to put in an a explanation (technobabble or otherwise) why all 72 torpedoes needed to be used. Perhaps a strafe run to wipe out the entire surface area of the planet to ensure Khan's demise. But then you still had 'innocent' Klingons there.
I just had problems with the whole incident. From Klingons being there, for there being the necessity to use all 72 torpedoes in someone else's territory, to Sulu being able to verbally broadcast his warning to Khan from space to 'an entire planet?'.
Seems to me they just wanted to have Klingons in the movie without a real reason. There was never a stage of mystery where I wondered if the Klingons were 'behind it'.