1) The colours of Spike's scales and body or Fluttershy's mane and body being interchanged. Not a cliche, but something that really annoyed me, like seriously?
2) Any of the mane six being loving each other romantically or all six of them having sex.
3) Pinkie's fourth wall powers being overused.
4) OC Mary Sue / Gary Stu Human/Alicorn/Human turned alicorn. Don't get me wrong, I wouldn't mind a human being turned into an alicorn when they get to Equestria but please, not a Mary Sue.
5) Derpy being there even though she's doing nothing just because the author likes her.
6) Dark backstories without the character even seeming to feel the effects of trauma for eg: lashing out, withdrawing into themselves, feeling guilty for no reason but because it's been drilled into them that everything is their fault, etc.
7) Human and pony having sex without the human being turned into a pony or vice-versa. How would you feel about having sex with a magical horse, however cute he/she/they may be?
8) Anon being used as a character.
9) Anthro
10) Main Character defeating all the villains without any difficulty. Remember, Twilight had to give up her magic before defeating Tirek, Chrysalis succesfully invaded Canterlot before she was beaten, etc, etc.