Revealing mistake: Near the end of the scene, when Bruce and Fox are in the tumbler Fox says "We never could get the damn bridge to work, but this baby works just fine" then Bruce turns the wheel to the left but the tumbler turns right. (00:57:45)
Revealing mistake: When Bruce Wayne is heading to the hearing at the courthouse, he checks his revolver to make sure it's loaded. His intent is to execute Joe Chill for killing his parents, so he would need a working gun. But when he opens the cylinder of the revolver to make sure it's loaded, you can see that all of the bullets have had the primer removed (the end of each bullet casing has a hole in it.) This is done to make each round impossible to fire, for safety on the set. (00:22:55)
Revealing mistake: When Bruce is told to execute the man in the ninja temple, watch the blade closely as he raises it up - the edge is ground down flat for the safety of the actors, he wouldn't be able to cut butter with that sword. (00:36:15)
Revealing mistake: When Batman flees from Gordon after their first meeting, he leaps across an alley and catches himself on the railing on a fire escape. This fire escape fails, dropping him (as well as the clothing left to dry on the railing). Batman grabs the next railing and again, this second fire escape collapses. Exactly the same as the first, with the same clothing falling off. When he climbs onto the 'third' fire escape, we see he's only come down one level, not two. The scene was artificially lengthened by using two perspectives of the same stunt. This isn't the same as showing one explosion from multiple angles because it is timed/edited precisely to appear as a longer fall in continuous time, not as repetition of the same moment.
Revealing mistake: As Ducard slides down the icy slope toward the cliff, a brief shot from Bruce's viewpoint shows Ducard from a top-down perspective, revealing that Liam Neeson has been replaced by a stuntman with far more hair and no sign of Liam's receding hairline. (00:40:05)
Revealing mistake: When the Batmobile is in the parking lot, there are skid marks under the Batmobile revealing the previous takes. (01:32:00)
Revealing mistake: When the train crashes and then explodes during the climax, there's several major flaws that give it away as a pretty obvious and unconvincing miniature. First, the scale of the fire and sparks aren't right at all. Second, the cars it crashes through in the parking garage don't move normally or receive realistic damage when they're impacted, giving them away as very small plastic models. (You can see at least two cars simply being shoved along unnaturally.) And finally, when the train-car explodes, if you watch carefully during the second shot, you can see the (supposedly concrete) ground ripple briefly in an unnatural way at the start of the shot, and even see the train car wobble at the end of the shot, again very unnaturally, as the pyrotechnics make the small-scale model move.
Revealing mistake: When Alfred is putting Rachel in the back seat of his car to drive her home, he fails to support her head. In the shot from inside the car, as he lowers her, Rachel instinctively and consciously stops her head at about 45 degrees and keeps it there until the shot is over. Had she really been unconscious her extremities would be limp and the momentum of her body being lowered would whip her head back, possibly injuring her neck. In the very next shot, Rachel is seen from Alfred's perspective, her body is already on the seat with her head only falling onto the seat from a couple of inches.
Answer: This is actually true to the comics, where a regular thug named Joe Chill was the killer of Mr. and Mrs. Wayne. There is no connection between this movie/series and Burton's "Batman"; they are separate takes on the same story, which is why things can be radically different. Burton chose to alter the storyline to give Batman an even greater reason to go after the Joker, that's his decision. Nolan chose otherwise in his presentation of the Batman legend, sticking to the original story.
Twotall