If there's one thing I really dislike about sci-fi and fantasy it's that often writers take too many liberties with the fact that those genres give their creators a lot of latitude to make up the rules on the spot. I really hate "magic" solutions to story problems. In a fantasy script, you might have a character solve their way out of a tight spot simply by having them produce a magic spell that negates the danger. In sci-fi, essentially the same cheat is used, except instead of magic incantations, the characters offer a lot of gobbledegook about "remodulating the main deflector dish to produce an inverse tacheyon pulse and an interplexing beacon."
Naturally, in something like Star Trek, it makes sense to come up with a certain amount of explanation for the "magic" properties of the space ship. As long as the writer doesn't abuse the basic premise too much, the audience will follow and it's fair to mine that science for drama. For instance, we accept that warp drive is what propells the Enterprise through space, and that the nacelles are what makes this possible. It's also fair to say that the engines somehow operate through the use of special crystals and a mix of matter and anti-matter to produce the needed energy to move the ship. Thus, if you're writing for Star Trek, and you decide to do a story about one of the nacelles being disabled in battle, or the engine crystals running, few people would probably call foul. Presumably, the drama is going to come from how the characters react to that situation.
My beef is when the problems are both created and then solved by the magic tech. You know the situation - when the Enterprise has become trapped in an anomoly and can't get out under it's own power. Captain Picard calls down to the engine room, where LaForge suggests they try energizing the main defector dish and produce a beam to get them out. He tries it. It fails. Then Data pipes up, offering that they could "remodulate" (everything on Star Trek: The Next Generation and Voyager can be solved by "remodulating") shield mutations to produce a static warp shell, thus separating the "time particles" of the anomoly from the "anti-time" particles which should cause the anomoly to collapse upon itself. Loo and behold, they try it and it works! Problem solved.
As a climax, that's pretty weak - and they might as well have had Data say "abracadabra" and make everything go away. And in fact, the writer's have all but admitted as such. But (as Mr. LaForge might have once said in a different life) "don't take my word for it." Watch this video of former Trek writer Ron Moore explaining how the technobabble scenes were written on the show.
I see the same sorts of problems now and then in sci-fi and fantasy specs written by first-time writers. Magic and magic-like advanced technology should only be the means for telling an interesting story - they shouldn't become the story themselves. Yes, every now and then a writer is going to have to fall back on using technobabble to get out of a problem, but if there's some solid character work, or that cheating is in service to a deeper story that develops the main characters, it will feel a lot less like a cheap gimmick.
Take a look at Star Wars. The climax hinges on the main character using a mystical power to shoot a torpedo into a small gap in a space-station's defenses. In the wrong hands, this easily could have turned into one of those TNG moments I decried above. However, in this case, Luke's use of the Force isn't just about the magic solving the big plot problem - it's the resolution of Luke's internal arc. He embraces Obi-Wan's teachings and let's go of his conscious mind. He reaches out and accepts that there are things greater than him. In doing so, he's able to perform a task that should be impossible. Thus, all that technobabble about the "thermal exhaust port" being only two meters wide and vulnerable only to proton torpedos that can't be targeted that precisely is all just to set the stage for Luke using this ability to accomplish what shouldn't be possible.
Good writing comes from the characters. It's easy to lose sight of that when you get into writing big epic space battles, or massive fantasy quests where a handy wizard is able to accomplish plotting miracles.