Audio problem: When Michael is forced to do "errands" for Brennen, they stop by Jonathan Carver's house to get numbers from him for a voice key. The code played back at the facility is 71348. He says "3" in a medium pitch (tone) at the house, but it is high pitched when played back at the facility; he says "8" in a medium pitch, and it's also high pitched later. And finally he says "9" in a low pitch and it's played back medium pitch. Also very obvious is the fact that Jonathan never says "1" or "7."
Continuity mistake: In the episode "The Education of Jaime Sommers", when Jaime and Tom are having coffee, the size and position of cappucino foam on Jaime's nose changes from shot to shot.
Plot hole: I believe in the very first episode, during the flashback when Mick remembers rescuing Beth and killing Coraline, we see him stab her with a wooden stake, which is supposed to paralyze a vampire, as said in the "Dr. Feel Good" episode. However when Mick looks back with Beth in his arms, Coraline suddenly gets up and watches him leave while burning to "death." This is simply not possible; in the "Dr. Feel Good" episode, Mick could not release the stake himself and asked Beth to do it. This also happened in the episode when Josef was staked by the hit man that was hired to kill him, (in the episode where we meet the woman, Sarah I believe, that he accidentally put into a coma after attempting to turn her). Again, Josef was unable to remove the stake himself and Mick had to do it for him, so there is absolutely no way Coraline would be watching Mick and Beth leave; she would still be on the ground possibly burning to death.