-Accepted Creepy Knoweldge. Because finding out someone has been secretly watching you and your friends for years, possible part of the future as well, is not creepy at all. Even if they don't get any intimate moments, well, you still are going to think Stalker, Spy, or something equally damning. Or I suppose they might try to pass themselves off as a seer, but that rarely happens.
~A subset of this is that people who know of a world as fictional don't actually have to explain it as such. Personally, I would explain it like this.

"Are you familiar with Seers, prophecies, or similar? Well, back on my world/dimension/reality, there is at minimum one, probably many more. Somehow, they are able to peer into other worlds, and possible other time. They see the stuff going on there, and write stories about it. This world is one of them. I already know a lot about it from those stories."

-Straw Vulcan. Because logic doesn't work that way. At all. Nor does anyone worthy of a character slot act that way unless in jest.

-Failure to actually use SCIENCE properly. Proper SCIENCE follows the SCIENCEtific method or something close, rather than, well, what Hollywood has deluded everyone else into thinking it is.
~Real scientists, on confronted with magic, will be Sceptical and disbelieving, up until someone starts levitating things. Then, after they make sure it isn't a cheap trick via transparent wires, they will try to figure out how to reproduce it. Eventually you end up with Tractor beams on your Starship.
~Arcane Howitzer had the guys from HALO carving Eldrich Runes onto their starships because, although they had no idea why it worked, it did in fact result in a hull plate with energy shielding. Hollywood has scientists going "This is Impossible, and gettings Logic bombed.
~Magic users are rarely better. They usually have no useful information on how magic works either. Admittedly, if you are gifted magic, or born with the easy version, instead of figuring it out yourself, with you having to know exactly how it works to use it would problems, It is understandable.

"I am having trouble discerning the real from mere folklore, superstition, and outright scams," the doctor admitted. "Could you perhaps assist me with that?"

"Me?" Sailor Moon pointed at herself. The sheer amount of books in the room was rather intimidating. "I only use magic," she said quickly. "I don't actually know how it works! I say the spell, something happens!"

Dr Mizuno frowned. "In that case, I would like to talk at some point to the person who taught you.

- MLP Specific
-Foalish. In the Pilot, Nightmare Moon uses the term repeatedly. All fanfictions I am aware of that use the term, use it to replace the word Foolish. However, I believe this to be in error.
There are many, many immortals in fiction. Most of them are Arrogant and see Mortals as lesser existences, to the point of classifying them as similar to bugs. Interactions often end up with Immortals calling Mortals various things, including Children/Child.
Nightmare moon, Like celestia is extremely long lived, if not ageless/immortal. This suggests that Foalish is actually analogous to Childish. As in Childish behavior would be called foalish behavior, as in behavior a foal would do.

-Violence Aversion
Aside from Fluttershy, the rest of the Main six are fully willing to use violence in the show. However, many fanfictions have them all be horrified by the idea of violence. And this is thier normal state, not while corrupted by discord or similar.

~All of them, save fluttershy fought the changlings, and with little hesitation.
~Rainbow dash, well, violence is pretty much her first response.
~Rarity, During the Pilot episode, she was the first one to attack the manticore.
~Applejack used what would probably classify as lethal force against the timberwolves.
~Pinkie Pie I can only think of her using the Party cannon against the changlings.
~Twilight. Well, I seem to recall, after Tirek destroyed the library, she went into rage mode, and started throwing nuclear-yield blasts at him. Repeatedly.

-Meat Aversion. Plenty of fanfictions suggest that Ponies are horrifed at the simple idea of an omnivore eating meat. Also, they tend to inaccurately call them carnivores. This is most commonly seen from Fluttershy.

However, In the show, Fluttershy specifically feeds some of her animal friends fish. That makes it pretty clear that there is no way she would have a massive aversion to the idea of eating meat.
Rainbow dash is secondary, since, as a friend of a Griffin, who are always either carnivores or omnivores (Cake + train episode suggests second option) there is no way she doesn't know Gilda ate meat.

By Eliezer Yudkowsky / Less Wrong

The (first) Three Laws of Fanfiction

Rule One If you do anything to increase the protagonist's power, or make their life easier, you must also amplify their opponent or add extra difficulties to their life. You can't make Frodo a Jedi unless you give Sauron the Death Star. Otherwise, even if it is well-written in all other ways, your story will suck because the reader will know to expect an unending string of easy victories, leading them to neither wonder or care about what happens next. The Mary Sue is not defined by her power being too strong, but by her challenges being too easily overcome.

Rule Two Originality isn't easy, but it is simple Just don't do stuff that's already been done. Even if all of your other characters are going to be absolutely true to canon, you still shouldn't have Harry Potter facing the same three challenges in the Triwizard Tournament because we've already read about them a thousand times. Put in three different challenges. Seriously. It can't hurt. Don't just go through the same events everyone has read about a thousand times before. Writing fanfiction lets you borrow the characters and the world; it doesn't exempt you from needing to surprise the readers and give them something new to read.

Rule Three The premise of a story is a conflict and its resolution - someone with a goal, which they take action to achieve, and severe obstacles that they must replan to deal with (not just speedbumps along the way), and some ultimate resolution of the conflict in which the people and their situation have changed. What happens if the Terminator is sent back in time to kill Voldemort is not a story premise, just a fleeting mental image. What happens if Harry Potter is under constant attack by shape-changing robot assassins is still not enough of a premise. Harry Potter is under constant attack by shape-changing assassins, and by the time he manages a spell to wall off the future he's already learned not to trust anyone could maybe be a story's premise (though you wouldn't put that in the summary, or tell any reader that until the story had ended). You can change this plan later - but you should at least have one to start with.

So if you have a lovely mental image of Frodo with a lightsaber

1. Figure out how to make his life more difficult, to make up for the lightsaber.

2. Decide what's going to happen differently in your fanfiction than in the other ones you've read.

3. Know what Frodo wants and what's going to get in his way, and have a plan for how it will all end.