I tried to rationalize this in a novel by suggesting that, entering the solar system from the outside, and counting backwards from the outer edge of the solar system, one could easily assume that Alpha Ceti V was Alpha Ceti VI if you had absolutely no reason to suspect that an entire planet had gone missing. Especially since, in real life, solar systems are huge and the planets aren't neatly lined up in a row the way they are in textbooks.
(Granted, this assumes that nobody used any long-range scanners to count the number of planets in the solar system, but why would they? Planets don't routinely disappear.)
As for nobody noticing that a planet exploded . . . well, space is
big and this system was supposed to be
way off the beaten track, which is why they were thinking of testing the super-secret Genesis Device there in the first place. It was a remote, largely unexplored system that nobody had visited for decades, so the planet's explosion went unnoticed.
It's not like Vulcan blew up or something.