Four major plot holes (the entire premise of the movie makes no sense)
1. Why was it necessary for the couple to leave their old life, severe all contact with family and friends and move to another town, merely to play a charade and pretend that Adam 2 was their first and only son? It makes no sense. If all they wanted to do was clone Adam, they could've easily disguise the process as a regular in-vitro (they actually do this in order to hide the truth to the medical staff) and pass Adam 2 as their second child. Even though he would physically resemble their first son, nobody would've guessed that he was a clone. They would simply assume that they had a second kid who happened to look a lot like the first one. It would be weird, but not impossible. They could even give Adam 2 the same name, since this is something that has actually happened in real life (a couple gives their son the same name as a previously deceased child).
I could accept the fact that Jessie could not conceive another child, which would make cloning the only viable option. But still, they could've easily hide this procedure from the rest of the world; if they can hide it from the very same doctors who perform the procedure, then it should be no problem whatsoever to keep it a secret from the rest. After all, IT IS almost a natural procedure, since we're not talking about a fully grown clone right from the start; Adam 2 is born like a regular baby and has a normal growth rate just like the original, so it's not like the memories of the first one would still be fresh to other people. And just because it's a clone, doesn't mean that he will behave in the exact same way. In conclusion: nobody would've even thought that Adam 2 was a clone, instead they would've merely thought that he was a second child born after a very risky in-vitro procedure.
2. The twist makes no sense either: up until then, we have believed that Adam's memories of his previous life were returning to him because he had passed the age he had when he died. This doesn't make much sense, but I can accept it as a horror premise, no big deal. However, once it is established that the memories he is recalling are from another kid, the entire premise falls apart. If they are from another kid, why are they manifesting now and not before? Is the movie telling me that the other kid was the EXACT SAME AGE as Adam (8 years, 1 day) when he died? That's just too convenient.
3. The way Paul finds out about Zachary's identity this makes no sense either: when he gets to Zachary's old house, the woman living there says that she interviewed a nanny who happened to work for that family. But when he goes to visit that nanny, she is obviously deeply traumatized because of her experience with that evil kid. Why then would she be willing to work again in the same house? It certainly would be hard to get over the whole thing if she has to work in the same place.
4. The ending that they used is stupid. Dr Wells did not have to go away. The fact that the Duncans still have Adam with them, and the fact that the newspapers don't mention Dr. Wells as being wanted by the police, shows that the Duncans didn't go public about the whole cloning procedure. They know that they cannot go public, because if they did, they would also go to jail, or at the very least they would lose custody of Adam, not to mention that the boy would see his life ruined because he would turn into little more than a media freak. You could argue that they have run away and gone into hiding, but it's obvious that they didn't do this, because they have the same names. They simply changed town (apparently they don't care that their son killed a boy or that he tried to kill his mother). Either way, it makes no sense for Dr. Wells to go into hiding himself, not to mention start looking for another couple: how is he going to do the procedure again? With what money? How is he going to do it without getting out of hiding?
Anyway, these are just some of the reasons why this movie makes no sense at all.