Or it incorporates and transforms the matter at the target location. Or something. They kept changing the explanations and theory all the time.

Drilling to the core of the planet in order to explode it is an old Dr Who plot, used more than once I think. At least they sort of excused it by making the villain an ex-miner.

I think the pseudo-science that bothered me most was the Enterprise escaping the black hole that Vulcan became. It was that same old Star Trek methodology: "We just make shit up."