During the sex scene at one point you can see Dakota from the back without a bra. Then as she grabs the blanket and sits up you can see that she is wearing a strapless bra. Then later when she is smoking and turns around again you can see that she isn't wearing a bra at all and is holding tightly to the blanket.
During one of the stripping scenes, Dakota's high-heel shoes change to black thigh-high boots.
Dakota's injured middle finger occasionally switches from her left to right hand until she gets her prosthetic arm which is on her right arm.
When Kenny Scaife starts to take off his shirt in front of Aubrey, he doesn't have a tattoo. In the following shots, a tattoo magically appears on his body.
Aubrey / Dakota's lips visibly get plumper towards the end of the film, as Lindsay Lohan had received Botox injections in real life during filming.
After the psychiatrist confesses to working for the police, Dakota threatens to stop talking, but then he mentions victim Jennifer Toland, and how her injuries were identical. She tells him to prove it, so he gives her graphic photos of Jennifer laid out on a slab, to peruse at her leisure. Dakota is now looking at the photos, all by herself. An FBI psychologist would never just hand over photos of murder victims and then leave. He'd want to be there, just to observe her reactions and use this as a means of starting a dialogue with her.
Glass tools of torture are a poor choice for amputating limbs, as glass, no matter how fine and sharpened they are, are not durable enough to cut through bone.
Jerrod meets Dakota at the Fleming's home after leaving the hospital, she proceeds to shake his hand with her prosthetic arm, which hurts his hand when it squeezes too hard. It's doubtful that the mechanisms in the hand are strong enough to hurt someone, even if they were, the designer would have certainly given it slip gears, or something of the sort, to prevent it from accidentally apply crushing pressure.
The killer starts to torture Aubrey by stuffing her hand in between two slabs of dry ice. Afterwards, he opens the clamp and lifts the ice, peeling the skin off the top of her hand. Aubrey reacts to this with understandable distress. However, it's unlikely that she would actually be feeling much pain, because an early symptom of frostbite is numbness, so she shouldn't be crying in pain.
In the biology classroom, the teacher asks if Jerrod can find the female reproductive organs on the worm, specifically if he can find the "seminal receptacles". Jerrod points out what he thinks are the female organs, but she informs him these are actually the male reproductive organs. She says the female organs are at the other end of the worm. Actually, this is incorrect because the seminal receptacles (female organs) are fairly close to the seminal vesicles (male), right around the heart.
When Dakota searches the internet for an explanation on her strange phenomenon she types the words 'bleeding wounds explained' into a search engine. This combination of words would not immediately bring up information on stigmatic twins.
During and after Jerrod and Dakota's sex scene, the entire bedroom is bathed in a blue light that doesn't seem to be coming from anywhere.
Aubrey is on a bench on school grounds, doodling in a sketch pad. Jerrod gives her a rose that was dyed blue. She pricks her finger on a thorn, and starts to bleed. Unless Jerrod dyed the roses himself, he bought them from a professional florist. Either way, a florist would have cut the thorns off of these types of roses before selling them, so she wouldn't have pricked herself.
When Dakota and Jerrod start having sex, Aubrey's mother can hear Jerrod's heavy groans through the ceiling. But up until they really get into the act, what Susan is hearing doesn't match the shots in the bedroom.
It seems unrealistic that the FBI would not have discovered Aubrey's story "Dakota" on her laptop any sooner after they had confiscated it.
The hospital could have compared birthmarks, moles, or any other manner of skin marks on Dakota to those they have on Aubrey's hospital records. Thus, Dakota's claims that she is not Aubrey would have been proven true.
The hospital could have contacted any friends or former employers of Dakota to verify her identity therefore proving Dakota's claims that she is not Aubrey.
Aubrey's boyfriend wonders how Dakota got her wounds if she's not Aubrey. At this point in the story, nobody has any evidence that Aubrey was wounded.
How did Daniel's scheme to switch his stillborn daughter with Aubrey at the hospital even work? This would mean that he somehow managed to convince the hospital staff to not only let him buy Aubrey off of her biological mother (who agreed to sell her since Dakota states that her mother kept receiving payments from an anonymous sender) but to also keep quiet about this and never once tell Susan that her baby didn't survive the birth.
When Dakota is on the bedroom floor watching the petals fall into the mirror, the shadow of a boom mic on the wall behind her is revealed in the lightning and quickly pulled out of frame.
The tape of the autopsy report for the first victim states that her fingers were cut off first, then the metacarpals (palm bones) were removed later. Given that when she is found her entire limb is missing up to her mid-forearm, how could the coroner possibly tell not only that the missing part was not all removed at once, but which bits were cut off in which order?
When the psychiatrist asks Dakota what her social security number is in the hospital room, she answers that she doesn't have one, because her mother was a crack whore. A quick look at the U.S. Social Security Administration's web page shows it would be easy for her to register for one herself. Seeing as how she didn't just up and become a crack whore like her mother, and tried to make a living like a regular person, getting a SSN would have been a logical first step.
It's pretty stupid of Dakota to think that she can simply stitch back on her rotting and dead finger without any form of medical assistance.
Once Aubrey is supposedly found alive after 17-18 days, Agent Phil theorizes that Aubrey escaped from the killer as the only plausible explanation, despite how far fetched it would be for a recently amputated girl missing an arm and a leg to be able to not only escape from his clutches but to also somehow find her way back home.
Dakota and Daniel had no actual proof that Douglas Norquist, Aubrey's piano teacher, was the killer. The fact that they turned out to be ultimately right is purely a lucky guess. Dakota only had two pieces of evidence to support her claim, Jennifer's trophy and Aubrey's ribbon from Norquist. None of this is actual proof that he came after them, as they received those awards for their exceptional piano skills, and a reasonable assumption for why Jennifer's ribbon is at her grave-site is that he left it there as a way to pay his respects, and not as a calling card.