When Spock says “Captain, we have a 94.92% chance of dying” when the chance of dying is 10%, I don’t believe the scriptwriter’s message is “probability is a crap science”, I believe it’s “Spock’s understanding of probability is crap, and he vastly overestimates it”.
Oh, Spock’s probabilities are probably quite accurate within the world of the story. The problem is that Spock doesn’t realize that he’s in a story, and by the power of plot, the ship and its primary crew are virtually never in real risk.
The other ships in the fleet aren’t so lucky—and indeed they are frequently lost, sometimes in facing the threats that the Enterprise deal with later.
The Enterprise-D was guaranteed to survive the first Borg cube, for example, even though virtually every ship that attempted to stop its course was destroyed. It’s the power of plot.
See: Huckleberry Finn, in which the protagonist believes he’ll go to Hell for helping a slave escape.