These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The Movie, which starts out as a recap of the first season then things start swerving off of continuity; and the events of The Movie never seem to be mentioned again. An Alternate Continuity where Endou could easily point at certain people he just met and exclaim they came from the future to help him win the Football Frontier sounds pretty confusing.
Also, Episode 100 when Hiroto and Kogure get lost in the woods, and are challenged to a match by a pair of Kappas, no character development happens, no new techniques are learned, and it's only mentioned in a blink and you miss it scene during a flashback.
The Kappas surprisingly enough make a brief cameo in Go's movie.
To be fair this is the only episode where she acts like this. She matures up a lot later.
Later on in the series, some of these traits seen from her arrival do get explained or at least get better elaborated. For example, her skill is probably due to being one of parents to the second stage children, meaning that she herself has to have the gene in order to pass it down Fei, especially since the second stage children are descendents are talented soccer players. We also do see a formal duel between Tsugiri and her during the France Era.
Fan Dumb: Especially those who think the Anime is more true than the Game. When the Anime is based on the Game.
Then again, the anime is following an one storyline unlike the game where everything is left up to whatever the player so desires.
Fanon Discontinuity: A lot of the fandom doesn't care for game canon because of how many different options available and a lack of "true story". Various things from the games they tend to disregard include Kazemaru's beatdown, the Kogure/Haruna ship tease (they substitute it with the anime's Tachimukai/Haruna ship tease) and Endou marrying Fuyuka in GO (Dark).
Kirino and Kariya, Tsurugi with either Tenma or Shindou until his Heel-Face Turn in GO!.
Good Bad Bugs: In Inazuma Eleven GO, when the game's graphics engine decides what direction to draw a character facing, acceleration seems to take precedence over velocity. In most cases, this makes perfect sense.note for example, one would expect someone trying stop quickly to both face and accelerate in the opposite direction of his velocity vector. But with the Slippy-Slidey Ice World physics of Snow Land Stadium, characters may be slowly decelerating due to skidding, meaning they should be facing the direction they're moving in but their acceleration vector is in the opposite direction. This causes characters to start moonwalking. Even if they're simultaneously dribbling the ball.
American fans are not happy with Level-5's No Export for You of the games and the anime, often having to import the games from Europe with the dreaded Dub Name Change. Even Latin America got the anime first.note Bonus points for being dubbed directly from the original Japanese instead of reddubing the EUR version, thus keeping original names and dialogs are as close as they can be.
It's finally come to America! ...Only the first one, cut from the compilation game and download only. Fans were less the thrilled.
The Korean fanbase (yes, such a thing exists) was not pleased with the appearance of Toyotomi Hideyoshi in Chrono Stonefor obvious reasons.
Scrappy Mechanic: The new scouting system in the GO video games, in which you need to obtain items and sometimes multiple other characters for just one. Also having to set off event flags to score goals, and a draw resulting in an automatic loss rather than extra time can rub people the wrong way.
Ships That Pass In The Night: Fudou/Fuyuka is the most popular hetero ship for both the characters and one of the most popular het ships fandomwise even though they never interact even once throughout the entire series. The ships popularity might stem from their similar names, relationship with Coach Kudou and fondness for...bananas.
One notable moment includes anything involving Ichinose.
Episode 45, full stop. Not only does Raimon lose horribly to Genesis with a score of 20-0, but you get the entirety of Fubuki's backstory and at the end of the episode, Kazemaru leaves the team. The episode is easily one of the most shocking ones.
Episode 46 is no better, with Endou having a massive Heroic BSOD over Kazemaru leaving the team, blaming himself for it and Fubuki's injuries and unstability, spending almost the entirety of the episode on the rooftop to the point he stops eating and won't move even if it's raining. And then Kurimatsu leaves, too, as he can't take the situation any longer.
GO Chrono Stone Neppuu/Raimei's final cutscene certainly qualifies. On his way back to the future, Fey visits Kinako, who is pregnant with himself, knowing already that Kinako will die giving birth to him. However, Kinako tells him that history can always change, and is optimistic that maybe she'll survive to see him grow up. The music just adds to the feels in that cutscene.
The Occult team in the first game. They show up really early, their an obnoxious difficulty spike in a generally easy game, they automatically score a goal and end the first half, to score against them in the second half you need to dance around a bunch of event flags (which is also disruptive to the game's atmosphere), oh and drawing against them is an automatic loss and gameover(!). Their a lot easier if you realize you should fire up and score a quick goal in the first half, but then they seem to demand a sudden knowledge of mechanics and flags very early in the game.
Inazuma Eleven 2 cranks the in-match scripted events Up to Eleven. The worst offender: Shin Teikoku. Sakuma shoots every ten minutes on the second, no matter which side has control of the ball or where it is on the field, effectively pulling the ball as far away from the goal as possible every ten minute, making victory basically impossible the first time around. You can retry the match after losing the first time and do it without events, but that should never have to be a requirement to proceed.
Inazuma Eleven GO while not as bad as the previous examples there is Dragonlink they do not qualify as this in story mode but when ever you play them afterwards. Their entire team is composed of avatar users which is not only intimidating, but they can appear faster then the game allows you to use your own avatars. Also they have a hissatsu technique that puts them right in the line of fire for goals without having much ability to defend against them.
They Wasted a Perfectly Good Plot: Tenma and Saru look surprisingly similar to each other and this similarity is even pointed out by Aoi. This is the only time when the similarity is noted and they never explain why they look similar.
Trolling Creator: After Gojou, who was a very minor character, hits number one position of the character polls (largely due to trolling) during promotion of the first movie. The creators decide to roll with that and place Gojou in GO as well. They even put Gojou's relative in another show by the same company.
Endou ends up with Natsumi but this upsets the Aki fans, might as well pair Endou up with Fuyuka in an alternative continuity to please them because hey, it's kind of similar!
What The Hell, Hero?: Its probably just this troper's view but in Inazuma Eleven Go Galaxy when Tenma was trying to convince other players to attending practice. When he talks to Morimura, she says her presence wouldn't make any difference to the team and Tenma just walks away. Sure, maybe most most people to walk away (being unsure of what else to say) but Tenma of all people does this. Tenma. The Endou clone. The one who constantly and successfully persuaded Shindo to reform the team. It would be at least in his character to try to end it at least something positive rather leaving it at just that.