Any author is capable of making a mistake, and comic book writers more than most. But comic companies aren't shy about changing things — or changing things back — to suit their perceived needs. Sometimes these errors, continuity problems or previous bad decisions are fixed quietly and/or cleverly. These were not those times.
1) One More Day
We might as well get the most egregious example out of the way. Back in 2007, Spider-Man had three problems: 1) by revealing his secret identity back in Civil War his life was even more fucked than usual, which led to 2) Aunt May being shot. The 3) problem was even more grave — Marvel editor-in-chief Joe Quesada hated Peter Parker's marriage to Mary Jane. The solution was, of course, for Spidey to trade his entire relationship with his wife to Marvel's version of the devil, Mephisto. Leaving aside the ridiculousness of a superhero making a deal with the devil — especially a deal that would destroy his marriage to a woman he presumably loved in order to buy his elderly aunt a few more years of life — the deal didn't even make sense for Mephisto. And then Marvel used it as a Get Out of Bad Editorial Decisions for Free card, erasing the public's knowledge of Spider-Man's identity, but also removing the crazy spider-powers (and organic webshooters) he was given during The Other arc, and bringing back Harry Osborn for no reason whatsoever. Apparently Mephisto wanted to throw in a few freebies! Thanks, Satan!
Back in the '90s, Hal Jordan had gone crazy, become a supervillain, and killed most of the Green Lantern corps. But Hal Jordan had a not-so-secret ally in Silver Age DC enthusiast Geoff Johns, who really wanted Jordan back as Green Lantern. So Johns decided that Hal had in fact been possessed by an evil yellow fear entity named Parallax who the Guardians of Oa had apparently trapped inside the giant Green Lantern Power Battery and never mentioned, even when Hal Jordan was calling himself Parallax and running around the universe killing people. While a very obvious attempt to erase Hal Jordan's career as a bad guy, it was a decent explanation for why the Green Lanterns' power rings had always had a weakness to the colour yellow, although why being possessed by an evil yellow fear entity would make Hal go white at the temples was a bit shakier.
The big reveal of Grant Morrison's run on the X-Men was of course that Xorn, the supposedly Chinese mutant with a star inside his head, was in fact Magneto in disguise; it ends when Magneto kills a great deal of New York City and Jean Grey, an enraged Wolverine decapitates him, and Morrison headed off into the sunset. I assume it was merely a day later when Marvel realised killing the X-Men's greatest and best-known villain was possibly not in the X-Men comics' best interests, and also they liked Xorn, so here was their brilliant idea: Xorn was just a dude who thought he was Magneto, and looked like Magneto and had Magneto's powers, and the real Magneto was fine and chilling in Genosha, and also Xorn has a twin brother also named Xorn with the exact same powers. This was nonsense even by the X-Men's ludicrous standards, and eventually Marvel tried to explain it in a 2005 Official Handbook of the Marvel Universe, where they essentially muttered "uh, Scarlet Witch did it."
4) Crisis on Infinite Earths
Just because a retcon isn't subtle doesn't necessarily make it bad. DC's Crisis on Infinite Earths was the least subtle comic story of all time when it debuted, and that just made it epic. CoIE made no bones about trying to clean up the massive amount of continuity problems and errors that filled the DC universe, as well as even simpler stuff like getting rid of the hundred or so surviving Kryptonians that seemed to be hanging out around the DC universe so Superman could actually be the last son of Krypton again. It pared down the DC multiverse to a single universe with one new, reasonably consistent backstory for each hero and villain (although things almost immediately got complicated again for continuity-challenged characters like Hawkman and Wonder Girl). DC Comics managed to get rid of most of its problems in a way that honored the comics that had come before, and was both entertaining and satisfying.
And if Crisis on Infinite Earths was the blueprint on how to revive your entire comics universe, Flashpoint was the "how not to." What seemed like a run-of-the-mill 6-issue Flash miniseries suddenly became the event that created the New 52, which rebooted the entire DC universe. After a bunch of DC universe-wide mega-events in which nothing really changed, suddenly, the Flash runs really fast and that somehow wiped out every thing that happened after Crisis on Infinite Earths — except, uh, Batman and Green Lantern, who stayed exactly the same and thus negated the whole idea. So superheroes had only been active for the last five years and the Justice League just had its first meeting and yet somehow Batman had time to mentor three Robins and have a son? Madness. The whole thing felt like a editorial mandate that had to be shoehorned into some event so it didn't seem totally out of the blue, and Flashpoint just happened to be the one going on at the time. Flashpoint did fix things in the sense that sales and interest in DC Comics went up, but story-wise, it created more problems than it solved.
Wolverine, like so many popular characters, had gotten overpowered, specifically in his healing power, which was essentially bringing him back from the dead every other issue. So Marvel decided he's been fighting the Angel of Death every single time he died in order to come back to life. Except then Wolverine's soul got damaged and he made a deal with the Angel of Death to fix it which somehow means if Wolverine actually dies again, he's going to stay dead (yeah, right). Obviously, having an eternal battle with the angel of death and a broken soul makes way more narrative sense than, you know, almost any other explanation you can think of, including "uh, Scarlet Witch did it."
7) Brightest Day
Comic characters come back to life in all sorts of goofy ways, but few are as obvious as Brightest Day, an event which brought back Aquaman, Martian Manhunter, Hawkman, Hawkgirl, Firestorm, Max Lord, and other assorted heroes and villains for a mysterious purpose by the White Lantern Entity, and that purpose was "DC wants these characters back." Each resurrectee had a specific task that the White Lantern Entity wanted them to accomplish, but why the White Lantern Entitygave a shit about what side Aqualad ended up on is unknown, or why it required resurrecting Aquaman instead of using someone who was already alive. Please note that whatever theWhite Lantern Entity wanted couldn't have been too important, because the whole damn DC universe was rebooted with the New 52 a mere year later anyways.