A lot has been made about the scientific inaccuracies and logical fallacies we often see in on screen science fiction. While no doubt some of it does stem from just plain ignorance or carelessness, a lot of it actually serves an important story telling purpose.
The first commandment of any form of entertainment is straightforward: You Must NOT Be Boring. This coupled with time constraints, limited budgets, and the need to tell a complete story driven by characters, has led to a number of shortcuts that creators of film and TV science fiction have to take. Its not that they, the writers, the FX crew, etc., are unaware of how scientifically accurate phenomena would actually work, its just that they have to put entertaining the audience and creating a compelling but easy-to-follow narrative first. And that often requires compromises.
This isn't to say that fans aren't right to complain about obviously stupid plot developments, or groan-inducing nonsense technobabble. Only that people should understand that science fiction is primarily about stories and characters first, and if some scientific accuracy has to be sacrificed to enhance either of those, so be it.
1. Cow Goes Moo, Duck Goes Quack, Space Goes Kaboom
In a dramatic presentation, music and sound effects are often used as dramatic punctuation, a tradition that goes back centuries to the earliest plays and operas. Its used so often because its proven itself very effective at evoking visceral responses from the audience. Should a filmmaker give up such a useful and versatile tool in a science fiction film simply because in real life, sound does not travel in space?
The answer is, it depends. Some very successful science fiction has used space silence as an effective dramatic device (2001, Firefly, Planetes). However, these works are almost always aimed at a more mature, thoughtful audience. For a more general audience work, especially an action-oriented one, such abrupt silences can serve to kill the dynamic flow of the story. So using sound in spaceshots, such as engine noises, weapon fire, explosions, etc, as well as background music, is forgivable if it all keeps the story or action flowing smoothly.
NOT FORGIVABLE: Humans breathing and talking in space without explanation (Superman IV, Power Rangers, for example). Even the most non-science-savvy of audiences nowadays know that people can't survive in space without spacesuits, much less go around talking in naked vacuum.
A sin scifi shares with many a modern crime show, this is where a computer enhances a visual image in some way that should either be impossible (how exactly do you enhance four fuzzy pixels into a complete mugshot?) or take many hours of tweaking and programming.
This is a necessity mostly born of time constraints. A typical scifi TV show only has an hour, not counting commercials, in which to tell its story. How much of that time do audiences really want to watch a computer operator clicking a mouse and typing at a keyboard to tweak an image into clarity? Even a montage of that would be fairly mind-numbing. So this is a quick little shortcut most scripts use to bypass what would be a scientifically accurate but very boring process to watch.
3. The Universal Up
In scifi TV shows and movies, most ships meet each other in the depths of space always oriented in the same "up" direction. Most combat, too, is usually depicted as two dimensional. Spaceships come at each other from ahead or behind, but rarely from below or from above.
This is mostly a visual shortcut, to avoid confusing the audience. Because make-believe spaceships come in a lot of unusual visual designs, they can be difficult to recognize from odd angles, especially during combat when they may be zipping quickly across the screen. This way the audience can more easily keep track of who's the good guy and who's the bad guy.
There have been exceptions to this, of course (particularly Return of the Jedi), but even then, with the fighters zooming about in three dimensions, the main fleets themselves were arrayed on a more or less flat plain in space as they exchanged shots.
4. And One Gravity For All
In science fiction, most locales are either one Earth-normal gravity, or zero gravity. There is no in between, even on the Moon or Mars or alien planets. Even the most low-tech future societies seem to easily develop magical artificial gravity.
The reason for this stems from the current limits of special effects and most movie/TV budgets. Simply put, all the actors and sets are on Earth, and there's no escaping that a full G is in effect there. Studios have gotten fairly adept over the years at visually fudging freefall with harnesses and other tricks, but these can get expensive, and are usually not used except for certain necessary scenes. In other words, faking anything other than Earth normal gravity can be a budget buster for most productions, so they usually use artificial gravity as a quick and easy end run around that.
5. Cosmic Wharrgarbl
Wouldn't it be convenient if every race, nation and civilization spoke the same language? In many science fiction universes, they do.
Yes, we know that the act of actually translating and learning to speak a completely new, alien language would be a long, complex, and arduously boring process to watch. Like with Enhance! this process is usually shortened dramatically, or even hand-waved away, to save on the audience's sanity and to get on with the story that will actually entertain them.
UNFORGIVABLE: Not providing even an arbitrary explanation for WHY everyone speaks the same language. If even my 8 year old nephew knows enough to question why everyone is speaking the same, then its not something audience members will just shrug away. Universal translators, babel fish, telepathy, a common trading language, etc., just pick one and move on. I'm looking at you, Stargate Atlantis. Earthers show up in a brand new galaxy that has been removed from human contact for 10,000 years and everyone can easily understand each other the first time they meet?
6. Ridged Forehead Syndrome
Aliens are one of the centerpiece concepts of science fiction. From everything we know about evolution, its easily a trillion to one odds that any alien lifeform will end up looking even remotely like us. So why do so many aliens in sci fi look like actors from Hollywood central casting with crinkly foreheads?
The simple answer is, of course, they are. Until fairly recently, expecting a special effect to act would be like asking the moon to dance a jig. If you wanted the aliens in your story to be actual characters instead of some barely-seen rubbery suit or glowy cloud, that meant you had to use human actors. And even Hollywood make-up masters could only make them so alien, especially with the budgets many productions had.
This has changed somewhat with modern computer animation (especially with incredibly convincing CGI characters like Gollum in the Lord of the Rings movies), but even so the process still remains very expensive. So ridged forehead aliens are still forgivable, as long as other measures are taken (language, mannerisms, culture, etc) to show that they're from a world other than earth. It is also forgivable if the presence of near-human aliens is plausibly explained away (such as in the Stargate universe, where many human populations were transplanted off Earth in ancient times to be used as slaves of the alien Gua'uld.)
UNFORGIVABLE: Having near-human/ridged forehead aliens in a sci fi production where the FX budget easily allows for better, less human alien characters. This is a sin especially perpetuated by japanese anime--being animation they aren't limited by FX budgets, and yet too often their aliens come in only two varieties--very human-looking or loathsome tentacle-beasts.
7. Outdated Special Effects
Now, we've all had a good laugh at one time or another at the Styrofoam rocks on the original Star Trek or the hokey muppet Yoda in The Empire Strikes Back. But seeing people put down the entire movie or TV show because of such special effects is definitely a sci fi sin.
We all know the story we're watching isn't real. But we're willing to suspend our disbelief for the sake of being entertained. Its why we can enjoy animated movies even though everything in the film is at least several steps removed from reality; its why we can get into plays even though its obvious we're just watching people shuffle about and talk on a stage with obviously artificial sets. If the story is good enough, whether the FX scenes look realistic shouldn't matter so much as how well they serve the ongoing story and move it along.
The original King Kong is a brilliant example. Does the Kong of the movie even closely resemble or move like a realistic gorilla? No. But is the movie still very entertaining? Definitely yes. The FX are crude by today's standards, but still serve the story of the film and move events along very well.
So this sin is very forgivable IF the special effects crew did the best they could with the technology and budget they had at the time. How well the effects serve the story should always matter more than how realistic they look.
UNFORGIVABLE: using outdated special effects on more modern films; in fact, the bigger budget and more modern a movie is, the less forgivable this sin is. Also, using special effects so much that they dilute the story instead of enhancing it, as was the case of all three Star Wars prequel films.
Let me know if I've forgotten any!