1) Joker breaking in and escaping the bank robbery with a school bus
When Joker robs the bank and his school bus plows through it's wall, that's about 3-4 minutes where the bus is just sitting inside a giant hole in the building for people to see while his henchmen were loading up the bus with cash. Joker even had time to make small talk with the bank manager and all that. He later exits through that giant hole in the building with the school bus, and again no one seemed to noticed. He then drives his bus in between other school buses filled with kids screaming (even the DVD's close caption subtitles points this out) in broad daylight with incoming traffic, while dust and asphalt were raining down the bus' ceiling, and again no one noticed.
2) Joker crashing Dent's party hosted by Wayne
So after Joker throws Rachel off the building to which Batman dives out of to rescue, both fall a number of stories and through a car, what happens afterwards? Did the Joker just leave the party and gave up looking for Dent? Did Batman forget that the Joker was still up at the party with a lot of innocent civilians? There was no closure to the scene. Next scene was at Gordon's office.
3) Batman slams his bike into the Joker's truck and falls off it, conscious perhaps
Joker's thug, rather than shoot a defenseless lying Batman (likely on the exposed mouth/chin area) decides to un-mask him. Fine. But in doing so, the thug gets shocked while touching Batman's cowl. So what does the Joker do? Rather than shoot him as well with his shotgun, after just seeing his own thug already get shocked, the Joker approaches Batman to un-mask him too! Into which Gordon comes out and pulls out his gun to arrest him.
First, that was just dumb by the Joker.
Second, Batman could've easily died twice in that scene if it wasn't for the Joker and his thug's stupidness. Argument is that Joker never intended to kill Batman. True. But Joker only revealed his intentions to Batman by the end of the film, and during this whole armored truck chase scene, Batman and Gordon didn't know that. All they knew was that Joker had already killed people including Judge Surillo, Commissioner Loeb, two civilians, and a guy dressed up as Batman with hockey pads. Joker and his henchmen could've easily shot and killed Batman at that point of the scene. Lucky for Batman, they were just dumb.
4) Joker escaping Gotham Central prison
So after Joker's capture, Gordon un-cuffs him so that he could be interrogated by Batman in his cell... okay... but after Batman finishes interrogating the Joker, they all just leave without handcuffing the Joker back. To make matters worse, not only was Joker un-cuffed but they stationed a detective INSIDE the cell to watch over him? Really? How about OUTSIDE the cell instead, that way Joker wouldn't be able to subdue the detective which lead to the escape? Not a strong plot device in the movie.
5) Wayne finding a thumb print by rebuilding a bullet destroyed splinter
Here's a hard one a lot of people didn't even notice. Wayne went all CSI basically reconstructing destroyed splinters from bullet to get a thumbprint. He did so by firing bullets from his computer controlled gatling gun into brick walls that matched his crime scene. From there, he just did an easy comparison of the holes in which his computer reconstructs the bullet's fragments rebuilding it, and super imposing it on the brick wall from the crime scene.
It's just that Chris Nolan forgot two basic simple CSI rules:
First rule: the thumbprints are left on the shell casings and not the bullet. The shell casings are ejected even before the bullet hits the wall (which Batman used as his crime scene evidence). So for Batman to find a thumbprint in a bullet hole was just magic.
Even if Nolan applied the first rule correctly, there is also the second rule: you must use the same bullet and the same gun for the whole thing to even be possible. Basically, it's telling us that Wayne got extremely lucky by finding not just the right bullet, but also the right gun, a gatling gun. So that basically means the men who killed Mr. Dent and Mr. Harvey in the apartment used a gatling gun that fires 4,000 rounds per minute, but magically used it to just fire a controlled single shot burst in the crime scene.
6) After finding out that the clowns are hostages, Batman calls to inform Lucious Fox
Wouldn't it have been easier for Batman to just call Gordon, or one of the authorities and their captains? If Batman is able to turn every single cellphone in the city into sonars, surely a simple phone call to the right person (rather than Lucious Fox) would've saved Batman having to battle the officers.
7) If Dent was found to be fallible, all the crooks he put into jail would be set free
Batman's exact lines to Dent during his interrogation of one of Joker's schizo henchmen in a dark alley - "If anyone saw this, everything would be undone. All the criminals you got off the streets would be released. And Jim Gordon will have died for nothing."
So all those 500 henchmen that Dent threw in jail will be set free, because Dent went on a little spree to go after the crooked cops that killed Rachel? Did the film forget that they all went through a court of law earlier, and they were all found guilty already? The only function it serves is another plot device to give Batman a plausible reason to take the blame.
8) Batman telling Gordon to put the blame on Dent's killings on him
Noble act at the end by Batman. But why even need to do that? Why can't Batman have just told Gordon to put the blame on Dent's killings on the Joker, or the Joker's men, or even some of the mob? It could even be made into a mystery homicide for now or even accidental because it REALLY was accidental. Now the public are supposed to believe that Batman killed Dent who had supported him in the media throughout the entire film? It didn't make sense throughout the whole establishment of Batman's character in the entire film. Batman was praised by the public, and after being a good guy for 99.9% of the film, they now have to believe Batman becomes a cold blooded killer in the last part of the film?