What I mean is, if they had a story where someone took over the ship's transporters and were using them to teleport the crew off the ship and we had this;
Captain: Cut the power to the transporters!
Officer: I can't! (Beamed away)
Then it would probably be considered bad writing that they just "can't".
^I wouldn't say so in that instance. In fact I'd say it'd be bad writing for that officer to go into a detailed technical explanation of why
he can't, right in the middle of a tense, dramatic scene. In terms of dramatic storytelling "I can't" is literally all you need. Of course the writer should know why he can't and should make sure that the rest of the episode is written with that in mind but the audience doesn't need to know.
B5 is I think a fair example of a show that had the science clearly thought out (as Earth tech was concerned) and was adhered to, but rarely, if ever was anything explained in anything other than in general terms. Most of the time it simply wasn't important or even relevant to the story.
Just like if you had a cop show, you don't have to explain how in internal combustion engine works every time they get into a car or what the inner workings of a semi-automatic pistol are every time they fire a gun. It's not relevant so you don't explain it, but (assuming the show is grounded in reality) you still have to portray those things as acting within certain parameters. The fact that those two machines are real while fusion reactors and PPGs are not is besides the point; I doubt a large proportion of average viewers have a clue why
either of those things work anymore than they really understand how a computer works. All that matters is they know how
it works (a more important distinction than you might think.)
In both cases that technology is part of the background fabric and has to be portrayed in a consistent fashion. What you don't have to do is constantly call attention to it but instead just allow it to be a part of the reality of the show. Cars go "vroom", guns go "bang", PPGs go "Vrrrrrrrrr" and cats go "quack."