How would they (Carol's staff of Starfleet) have known which planet Ceti Alpha V really was, since it no longer resembled the world it had been? Also, how many records would they have had of that system in its' previous configuration?
Also: Kirk didn't exactly let Starfleet know that Khan and his crew were left there. So you can't really blame Reliant's staff for not knowing to avoid there.
As for the "tainted cookie" example: I'm sorry Treadwell, but that's not the same thing. Genesis was complete enough to be used because David Marcus took a dangerous shortcut. It would have been useless to Khan incomplete; Khan only learned of it because Captain Terrell and Chekhov were captured by Khan and implanted with Ceti Eels, and forced to tell Khan why they were there.
They would not have been there if Genesis were not ready to be tested, and that would not have taken place (by David's own admission) unless he had used protomatter to "solve problems". There may have been "infinite factors" involved, but only a select handful of them led to the fateful events of ST:II TWOK...
...and the catalyst was David's use of protomatter, making Genesis a viable system at a time when Khan (and later Kruge) could get at it.
I agree… there’s a big science mistake on a planetary level here. The filmmakers basically had to waive their hands, state something as fact, and move on without anybody questioning it. Ceti Alpha 6 exploding with leave a large debris field, that certainly would’ve been detected by ships entering the system. And remember, we’re only what less than 20 years out from when Khan was exiled in the first place?
if we assume that Kirk colonizing Ceti alpha 5 with Khan and his crew was clandestine (Space Seed), and kept from Starfleet so that nobody but the Enterprise crew knew about it… but why would Kirk have done that, kept his secret from Starfleet?
If Starfleet already knew of the system then they probably had it mapped; there would be one less planet than you expected when you came back into the system, and the planet you went to would have a different orbit than what you expected.
And there’s the continuity error with Chekov. During the original series/space seed, he was not yet a member of the crew. So he would have no firsthand knowledge of the events of Khan and their exile to the Ceti alpha system. However in Star Trek 2 checkov immediately recognizes the Botany Bay, knows that Khan might be around, and it’s an emergency to escape. He then talks about Khan and Kirk as if he were there. Khan even says he never forgets a face, and recognizes Checkov and eventually remembers his name.
Which changes the canon, meaning that Checkov knew about Khan all along, at least in the continuity of Star Trek 2. Which also means, when they came into the system, Checkov would’ve known about Citi Alpha 5 versus Alpha 6.