An anime usually starts while the manga is still being produced. This is for a number of reasons, including riding the coattails of the manga’s popularity; and also, the anime should provide a marketing benefit to the original manga’s creator. Although they have that mutual agreement, generally, the anime and manga production are done with very little mutual oversight.

Anime productions studios need to deal with this problem, usually by slowing down the progression of the story or just inserting a filler arc. Fillers can be a good way to give screen time to minor characters or flesh out canon relationships, but they can also produce inconsistencies.

In Bleach, Ichigo will attain immense power to defeat an extremely powerful enemy, sometimes killing them with no ethical remorse. The filler arc ends. The power, the victory, and the ethically unsound behavior are never to be seen or mentioned ever again. Instead, we return to general assumptions of Ichigo being generally good guy, second-class pseudo-shinigami, despite everything that happens in the filler arc.

Many fans are accepting of filler as an inevitable consequence of production timing, but ideal timing isn’t something of fantasy. In the case of ERASED (Boku dake ga Inai Machi), the anime and the manga came to their conclusions at about the same time, with the conclusion to the manga being in print just before the conclusion of the anime would air. Although very tight, the author agreed to work with the animators and let them in on the ending in advance. Thus, ERASED was safeguarded from an adaptation-induced plot hole, avoided a potentially angry fandom, and was rewarded with a generally positive reception.

Speaking of The Conqueror of Shamballa, this and many anime just need more explanation or at least a tiny bit of reasoning to keep us from having to figure it out all on our own. We could use a little more explaining with the Gates in Darker than Black. We’re still waiting for answers in Attack on Titan, but maybe they will come. Then, there are the character questions. If Shiba Tatsuya doesn’t want to be noticed, why does he go out of his way to prove to everyone he is OP in The Irregular at Magic High School? Also, in Beyond the Boundary, the contradictions in Kuriyama’s motivations and actions make the plot twist hard to swallow.

Creators appear too lazy or disdainful of restrictions to give a proper explanation, and then the plot goes in way too many directions, simply because there’s nothing canon to contradict what’s going on. These aren’t necessarily plot holes, but unanswered questions hurt all the same and represent shoddy storytelling that veteran anime watchers have come to ignore or despise.

We’re not saying we always need an explanation. As long as the story can stay within its own rules and logic, regardless of how fantastical that world may be, we can accept the fact that Satoru slips in time in ERASED. Hypothetically, suddenly revealing, “It was all a dream” could very well ruin the whole story for an anime like Grimgar of Fantasy and Ash. Sora and Shiro are transported to a world of games in No Game No Life? Cool, no problem. What’s going on in Paprika? Never mind. It’s cool. Detailed explanations in these situations could be disappointing and more confusing than without them. Nonetheless, some series need a little more explanation, especially when the plot points start to become too confusing for enjoyment.

There’s a convention in anime, when someone conveniently forgets something to make an episode or a scene more powerful. In Dragonball, Goku hesitates of fight Piccolo, because Piccolo’s death would mean the death of Kami. He only fights him under the assumption that Kami can be revived with the dragonballs. Later, Goku insists not to kill Piccolo, because if Kami dies as a result of Piccolo dying, the dragonballs will disappear. Wait, so Goku knew all along and fought him anyway. That’s brutal. What was the initial hesitation about? Well, in this case, Goku forgot something extremely important, i.e. he got hit with the stupid stick.

Although rampant in shounen anime, romance anime has its share of characters suddenly losing the ability to remember important things, particularly, if a person likes them or not. In Wolf Girl and Black Prince, even though Erika got the Christmas present from the guy she likes, she still backtracks to, “Does he still like me?” Forgetting stuff sure does help the emotions stay high and tight. In a combination with filler-caused inconsistencies, in the second season of Noragami, when Hiyori promises Yato that she will never forget him, we cough-laughed thinking back to the Rabo Arc, a.k.a. season one filler, when she totally forgot his existence.

When it comes to science fiction, it’s pretty acceptable that the fiction part can play a big role in any given part. Nonetheless, despite how inspiring some inventions can be or how much you love science, it’s a stretch to say “science” when you actually mean “magic.” For the most part, we can be fairly forgiving about this issue. Anti-gravity boots in Ao no Kanata no Four Rhythm seem great! We all get that Gundams are inefficient, but giant humanoid robots are a win! Considering we don’t fully understand black holes, sure, Steins;Gate, no problem! Still, when we get a person solving 512-bit encryption with the pure brainpower in Summer Wars, we’re pretty sure that’s most likely not scientifically possible. Then, when a company can somehow make very lifelike emotion androids but can’t seem to find one of a thousand plausible measures to make them not berserk in Plastic Memories, it’s hard to say if that’s really advanced technology or just trying to implant the science trend into an otherwise good idea.

Fan service doesn’t always cause plot holes, but it does sometimes in a number of genres. Forced injections of head crashing into a girl’s chest aside, outrageous situations in ecchi anime that would normally induce a least a little interaction or relationship development are usually just thrown to the wayside as if they never happened. In coordination with the stupid stick issue, princely interaction fan service can easily cause repetitive situations, seen throughout Kamisama Kiss. Even in military “tankery” fan service anime, Girls und Panzer, the harsh reality is that some of these tanks wouldn’t even be able to put up a decent fight against the more sophisticated tanks. If this was a really a sport, all the teams would probably be using the same tanks, you know, the best ones.