Star Trek is big. Big spectacle, big sound, big cast, big budget.
And it doesn't make a damn bit o' sense.
Let's say- for instance- that a character renowned for his logic makes an emotional, illogical, and almost certainly illegal decision and sends another crew member down to a zombie glacial planet, where he will (of course) meet Simon Pegg. Only the zombies, this time, will not be the Shaun of the Dead traditional zombies, but Resident Evil abominations. And, um, let's further say that a meganormous wolf-baboon is hard on the heels of this crewman- but a mutant blend of spider, dragon, and venus fly-trap kills the wolf-baboon. But instead of eating the larger baboon, which it has already killed, it instead chases the much smaller crewman.
Let's also say there exists a substance which will create black holes. A minute amount- a drop- of this substance is all that is required. Instead of taking this substance in a pre-packaged, ready to use platform, this super-advanced civilization instead takes an enormous amount of this substance on ship, necessitating an overly-complicated, long preparation process that seems more at home in the early 20th century. Let's say that all bad guys are handily identified with villain-y tattoos, and that any evil ships look like they're made of rusty razors and bad attitude. Let's say that anyone involved in a fight will automatically get into a fight utilizing their strengths, no matter how unlikely those skills are...well, you get the point.