The most obvious plot hole of all
Firstly, I want to say I thought this was a really excellent film. Yes, there are plot holes but for me they were trivial, at least whilst watching the film. Unlike such nonsenses as Flight Plan and Arlington Road where the holes continually detract from the film.
However, there is one very major plot hole (unless I have seriously misunderstood something).
If we are to believe that the paedophile's father was so desperate for revenge on someone who merely provided an alibi for his son's murderer that even eight years later he would have wholly innocent people tortured and murdered just on the off chance that the witness (Margot) was still alive, why the hell is the alleged murderer still alive and openly living locally?