MarkB
Legend
The usual numbering convention for planets is to start from the closest to the sun and work outward, so if planet 6 in a system disappeared, that shouldn't lead to planet 5 being mis-identified on a subsequent visit.Not sure what you mean here? The misidentification of Ceti Alpha V as Ceti Alpha VI is a plot point in the film.
Possibly Starfleet number them a different way, or possibly Ceti Alpha VI's explosion pushed Ceti Alpha V out beyond the orbit of what was formerly Ceti Alpha VII.
Honestly, though, there's no easy way to justify it - this was clearly a surveyed system, and a Starfleet crew specifically looking for planets meeting a particular specification has no excuse for not noticing that the planets in the system no longer match up to what they have on record.