Batman (1989):
*Batman being unable to hit the Joker while shooting at him from the Batwing, yet the Joker is able to bring down the Batwing with one single shot (via a very long pistol). Maybe, Tim Burton was trying to display a sense of comedic irony, but even so, the whole sequence must require to viewer to supsend a sense of disbelief that's extreme even for comic book movie standards.
I always took that as a play on the fact that, in the comics, it seems almost impossible to kill Joker. You could have him crash into the ocean in a helecopter just as it explodes with a few dozen pounds of C4 inside and he'll be right as rain a few issues later.
*The infamous "Your nose could be gushing blood!" scene involving the Penguin and Josh. Batman Returns as a whole just came across as one "big lipped aligator moment". It to me, is like the first movie (just replace the Joker with the Penguin, Vicki Vale with Selina Kyle, and Carl Grissom with Max Schrek) on acid.
I'll get to the "gushing blood"/political plot-line in a second, but I think what you mentioned at the end with the "last movie on acid" bit was very intentional by Burton and co., espicially with the final sequence:
In '89, Batman & Joker, whom ultimately "made" each other into the monsters they are, fight for revenge while Vikki Vale, the woman who loves Bruce/Batman, watches on in horror.
In Returns, we have Shreck and Catwoman, whom was "made" by Shreck into the monster she is, and takes her revenge while Bruce, who loves Selina/Catwoman, watches on in horror.
*Batman referencing Superman ("This is why Superman works alone!"
) in the opening sequence. It seemed as if, they were trying to break the fourth wall by acknowledging the other big comic book superhero.
To be fair, Batman & Superman, in the comics, are in a shared universe, and Superman has been in plenty of Batman comics, even the well-liked/influencial ones, such as Death in the Family and No Man's Land.
*Mr. Freeze's puns relating to the cold. Just like what I said before about Two-Face and the coin, this simply reinforced the idea of the otherwise tragic Mr. Freeze being a gimmick villain rather than something more complex.
I agree that the puns were bad in the movie, but Freeze had many cold-puns in Heart of Ice as well. I think the difference is that in Heart of Ice, he is relatively emotionless/melacholy. I wonder if Schwartzenegger was directed to play it more like The Terminator instead of Commando, he would have been better.
When the Joker announces that he is planning to blow up a hospital, nobody thinks of looking in the one with Dent.
Uh...they did. The whole hospital was abandoned, with the exception of Dent after Joker manipulated things.
I'm glad someone mentioned Penguin's nose bite scene. I know that in the world of politics there is a lot of cover ups...but REALLY? Also, this burtonized verision of the Penguin running for mayor in the first place. This random unknown weirdo comes out of nowhere, runs for mayor, and he is acctually getting votes? Are you kidding me?
To be fair, Dubya's biggest job he took before getting into politics was failing to find oil in Texas. Plenty of people are not the brightest when it comes to politics.
Here's one from Begins: The Microwave Emitter. That just takes a good, long, satisfying piss on basic science. When there are microwaves, they heat up EVERYTHING in sight, not just water, I don't give a damn how "focused" they are.
This wouldn't have bothered me so much, if it weren't for that not only did they promise a hyper-real world, where the only difference is a guy being able to fight crime without getting killed/arrested on his first night, but the science and tech was already solid from what they used to make Batman's suit. It was definately a dropped ball in that department.