Ass Pull: Rouge suddenly becomes evil with no explanation or foreshadowing for why she is evil. Courtney complains about this.
Crack Pairing: Amy and SNT is arguably the most popular pairing (although SNT and Rookie, a not-Crack Pairing have definitely been giving it a run for its money). Keep in mind that for most of the series, Amy hated SNT.
Amy was trying to get rid of SNT for most of the series. But in the ending, fans decided otherwise, and Amy and SNT became the Official Couple (although going by Forces and Amy still being a Tsundere, they most likely arent together in that series).
Infinite of all people starts falling for SNT in the series, SNT Forces. It starts off pretty one-sided, with her understandably being terrified and creeped out by him, but during her and Sonics final battle with him, she comes to the understanding that theyre Not So Different after all (being created to be the ultimate life forms) and that she cant find it in herself to blame him for war in general (although this one IS his and Eggmans fault). Its heavily implied hes trying to kill her to rid himself of his feelings, and in the end it holds him back and allows her and Sonic to fight him off, after which he is forced to teleport out once his feelings for her grow even stronger.
Launcher of a Thousand Ships: SNT ends up becoming this. So far, she has been shipped with Sonic and Shadow. In the ending, she even gets shipped with Amy thanks to popular demand.
Les Yay: In the finale of the sprite comic series, Amy kisses SNT very briefly. We dont see the reaction of the latter, but she didnt seem to mind, although they are still just friends in SNT Forces.
Memetic Mutation: SNT should not be able to do half the things she does, but she does them anyways. How? Because she's SPECIAL! Alternatively, it's OC Black Magic.
Why didn't [character] die from something that by all accounts should have killed them? Because they're made of PLEXIGLASS!
It seems that Rouge was working for Eggman this whole time.
Apparently, Knuckles is sexist. And he is also willing to work for Eggman when the doctor gives him the ability to control fire and proposes that he use it to get revenge on SNT. Even though SNT only beat him up so badly because Knuckles underestimated her and mocked her in the first place.
Wangst: Sonic becomes disturbingly obsessed when SNT goes missing. Even Courtney lampshades it.
Writer Cop Out: It turns out that the sprite comics were never finished. Later averted when Courtney does a livestream specifically to give an ending to the series.