There are lots of ways to write a bad fanfic, most of which are self-evident. If you can't construct a comprehensible sentence, that puts a pretty low ceiling on your writing quality, to go with an obvious example. But what are some of the more minor yet insidious pitfalls to which a writer can fall prey? More than that, what are some pitfalls specific to MLP?
Head below the break for my thoughts on what semi-inobvious mistakes can ensnare an unsuspecting ponyfic author. These aren't major plot decisions or basic construction questions; rather, they're the "little things" that can take a reader right out of a story. They're self-inflicted wounds which are frustrating to see precisely because avoiding them wouldn't involve a complete re-write. Now, without further adieu, my top five.
5. Gratuitous Real-World Swearing
It's certainly possible to write a story set in the MLP universe which involves swearing from one or more characters; this isn't about that. This is about main-six slice-of-life fics where Rarity pricks herself with a needle and shouts "Son of a b****!" Likewise, it's about show-tone stories that inexplicably drop f-bombs. The only thing more stunning than how obviously poor a decision this is is the frequency with which it happens. Remember: word choice in dialogue is an important part of characterization. Unless you're doing enough groundwork to justify harsh expletives being added to a canon character's vocabulary, this is just another form of characterization failure.
4. Using Inappropriate Regionalisms
This is when a character who is obviously not Australian (or who obviously doesn't have an Australian accent, rather) talks about grilling on his "barbie," or when a character who doesn't have a Southerner's voicing gets a drink from a "bubbler." It's when any character uses vocabulary from outside of their region ("General American" for most of the canon cast, with the exceptions largely being obvious). This can actually be a difficult thing to avoid in some cases, where authors simply don't realize that a common-to-them word or phrase is in fact highly localized, but there are few things more distracting than having Applejack say "I shan't."
3. Forgetting Pony Anatomy
As humans, we're awfully used to talking about holding things in our hands; ponies don't have those. Leaving aside the question of how dexterous pony hooves "should" be, let's at least agree to call them hooves, eh? Ditto "feet," "arms," and so on.
2. Pointless Modern Tech
In the show, the tech level varies as is required by any given joke; computers and video games can exist for the sake of a sight gag, and so it's hard to say they can't be in a story. But if you're going to use, to pick the obvious example, cell phones in your story, at least do something with them. Notice that all the show examples of modern tech exist for very specific storytelling purpose; we've never seen a character use electronics "out of focus," so to speak. In other words, if you absolutely must have cell phones in your story, at least make sure that you absolutely must have cell phones in your story!
1. Ponies Not Knowing What Hands Are
This is painfully common--to this very day!--in HiE/PoE (Human in Equestria/Pony on Earth) stories, for no reason I can readily comprehend. Ponies know what hands are. Counting handlike claws, we've seen griffons, dragons, and more come wandering through Ponyville. Ahuizotl has hands literally out the wazoo, and he's a major character in Equestria's most popular book series! So when a pony sees a human's hands, and describes them as "soft-looking hooves with more little hooves coming off the ends," or "fleshy lumps with five short tentacles" (both of which I'm pretty sure I've seen used unironically, but am admittedly writing from memory), it's just silly. It's the sort of description a pony would never make, and even if a pony had somehow never seen nor heard of "hands," those are some frankly ridiculous descriptions; they'd probably just call them "claws." After all, imagine you didn't know what a squid's appendages were called; you wouldn't call them "ten long boneless hands," would you?
...Note that this list is by no means exhaustive; I'm sure I could easily come up with five more minor-but-easily-avoidable, pony-specific things not to do in your story. Still, if we could all agree to quit doing these, that would be a wonderful start.