Revealing mistake: When the penguins emerge to carry the Penguin (character) to the water after he dies, the penguins are blatantly little people in costumes. Their "skin" crinckles unnaturally, and the spot where their arms meet their bodies is very flat and fake-looking.
Revealing mistake: When Batman is driving the Bat-boat, just after he dodges the two rockets the penguins launch at him, as the Bat-boat slams back down into the water in the background, the scale of the water-splash reveal that this effect was achieved using a miniature set and miniature Bat-boat model. The scale of the water splash, and the enormous "drops" that splash up give the effect away.
Deliberate mistake: After Batman destroys The Penguin's controlling system and breaks the TV screen he is 4 meters away from a narrow alley. Shot changes and he's now downtown driving around the city, Then there's a POV shot of him driving towards the narrow alley again, though he is now many meters behind. Then back to shots of him driving downtown until he finally arrives at the narrow alley. It adds up for pace, but it's very awkward indeed.
Continuity mistake: When Catwoman exits Schreck's she's doing flips without hells. After the explosion, when she climbs the wall heels appear.
Continuity mistake: When Selina arrives home at her apartment, she is wearing a brown suit, and then rushes back to work. When Max finds her looking at the files, she is wearing a gray suit with a shawl.
Continuity mistake: In the opening, Penguin's parents look at the cage holding him. From the outside, his shaking is making the cage move slightly side to side. From inside, his shaking is not moving the cage at all.
Revealing mistake: There is a shot of Batman driving the Batmobile around town late at night looking for The Penguin. In this shot, look at the cars parked at the side of the road. They are miniatures as well as the rest of the shot.
Revealing mistake: When the penguins launch the rockets/missiles in the end, watch carefully. In the second wideshot of the rockets launching (right after the bats begin to attack Danny DeVito), you can see two of the rockets hanging in midair, not moving. At the beginning of the shot, you can even see one of them spurting some fire. The rockets (attached to visible guided wires by the effects crew) got stuck in mid air right before the shot began, a few seconds before this second volley of rockets fire off.
Revealing mistake: When The Penguin (character) is first introduced, feeding the other (real) penguins, watch closely. While some of the penguins are real, it's blatantly obvious that some of them (particularly the ones to the left of the screen when Penguin says "Hi") are animatronic puppets, as they have very unnatural neck movements and don't waddle around like the rest. A few shots later, when Penguin says, "I believe the word you're looking for is...", you can even see an animatronic penguin on the left side of the screen that is unnaturally leaning slightly forward, yet never falls, revealing it's a puppet that was mounted to the ground.
Continuity mistake: When Oswald Cobblepot is in his crib as a baby, in outside shots the rubber duck on the string is swaying back and forth. In shots through the crib bars, it is dead still. (00:01:00)
Answer: Nothing was stopping them. After Penguin's true nature was revealed, they most likely started searching the entire sewer system but couldn't find where his lair actually was so they had no choice but to give up.