1. Storm's Line (you know the one) in X-Men Was Supposed To Be A Snarky Take On Dad Jokes
Listen, no one's trying to defend the X-Men series portrayal of Storm - she's a pretty nothing character who's never given any significant motivations or relationships to play off of, and that's the fault of the writers and directors, not Halle Berry. But all parties involved got A LOT of flack for the line "Do you know what happens when a toad gets struck by lightning? The same thing that happens to everything else." It's a weird one-liner - not clever, not funny, takes way too long to say, etc. But the real problem is how dramatically it's delivered - it's treated sorta like the culminating moment for Storm in the film, her big Shakespearian monologue moment - when it was supposed to be a dad joke.
In case you're not familiar, the joke ACTUALLY is supposed to be "Do you know what happens when a toad gets struck by lightning? IT CROAKS!" There's a 95% chance your dad is telling you this joke RIGHT NOW.
Storm's like was meant to be set-up like she was telling that goofy dad joke - but then instead of the pun-tacular punchline, she shrugs it off. "The same thing that happens to everything else" is basically a "duh" shrug, not a grand proclamation.
The line (the original line, that is) was infamously written by current Marvel-god Joss Whedon, who had this to say: "HAHAHAHA NO ONE CAN CHANGE MY SCRIPTS NOW!" as he forced former Fox-executives to battle to their deaths in a Roman colosseum using only DVDs of Serenity.
2. Willem Dafoe's Green Goblin Mask Originally Looked Like...The Green Goblin
Here's a weird decision - you cast Willem Dafoe as The Green Goblin (since Willem Dafoe has a naturally terrifying face - and also his last name means "The Foe"), but instead of letting him use his own facial expressions and natural terrifying-ness, you cover him in a goofy Power Rangers mask shaped sorta like a goblin. That's because the original animatronic Green Goblin face was a little too realistic and creepy for the family audience Sony was shooting for. They compromised with the helmet you see in the movie - which is pretty bad, because it prevents you from seeing any part of Willem Dafoe's face for the duration of his performance (and a LOT of acting lies in facial expressions) and because we're made to believe OsCorp made this freaky Halloween mask for glider pilots to be used by the Armed Forces? Weird call.
That being said, the original mask wasn't perfect, but with some CGI re-touchings, it could have looked pretty darn cool. Luckily, the film made up for this one slip up with the timeless fame of Macy Gray and the raw charismatic sexuality of Tobey Maguire.
3. The Ending To Superman Led Directly To The Sequel, Instead of the Dumbest Time Travel Plot In Movie History
The original Richard Donner Superman film is still probably the best depiction of DC's iconic hero in a live action film - and is responsible for making comic book movies a thing that exists. That being said, the ending of the film (where Superman reverses the rotation of the Earth by flying around it super-fast and that somehow turns back time - instead of, ya know, killing all life and wreaking havoc on every ecosystem on the planet) is pretty dumb.
What makes it even dumber is that there was originally an ending planned that would have avoided the whole weird time travel plot AND provided a direct link to the sequel - the missile that was due to strike the San Andreas Fault would be deflected by Superman and knocked into space, where it would detonate...and the explosion was the reason Zod escapes from the Phantom Zone. It would have tied up the movie nicely, ended on a really cool cliffhanger, and taken care of some unnecessary exposition in the sequel - since pretty much the EXACT SAME THING happens in Superman II to open the Phantom Zone.
They changed it because Donner felt it would be too "gimmicky" to use one film in order to lure folks back for a sequel and wanted to leave the first film with closure...even though they were shooting Superman II simultaneously with Superman I, so there was almost no question that they were expecting audiences to come back for more.
Luckily, Superman III and IV came out not long after, and any complaints about dumb stuff in Superman I was overtaken in Superman III that's mostly about Richard Pryor inspiring Office Space and Superman being a dick and straightening the Leaning Tower of Pisa.