Plot hole: When the two henchmen who break into Nick's loft to kill Lisa are captured, the case is closed. But the two thugs were reporting back to a boss who wasn't caught, and who surely would have sent more hitmen after Lisa. So the case shouldn't have been closed.
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Plot hole: Nat thinks Nick is becoming more human because he can see himself in the mirror, and he replies, "Only sometimes." This line contradicts series canon, as "Forever Knight" did not adhere to the vampires-don't-appear-in-mirrors cliché. Nick was seen to reflect very nicely, in fact, every time he passed a mirror, and not just "sometimes."
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Plot hole: Near the end, a cop comes to tell Schanke that an explosion has been reported at Nick's place. But neither of the two intruders uses any explosives. One shoots his way in through a door and the other breaks in through a skylight. Neither makes enough noise for the disturbance to be called an explosion.
Plot hole: The insertion of a musical sequence used to fill extra time in this episode creates a plot problem. It's spliced in between Nick's urgent plea for Nat to stall the autopsy and his rescuing the bound and gagged Rebecca, and unfortunately makes it appear that in that interval, Nick simply went home, played music and sat in his loft window brooding, ignoring the case altogether.
Plot hole: At the Precinct after the second spa incident, Captain Stonetree refers to "two unexplained reflex murders in one night." But the first victim survived the attack - so there was only one murder, not two. A little worse than a simple character mistake, since he's the police captain and knows the case. Schanke gets it right later, when he says, "One murder and one attempted murder."
Plot hole: In the morgue, Nick tells Nat that vampires disappear when they die. Not so in this series. "Forever Knight's" vampires, defying old movie clichés, remained stubbornly intact when staked, making Nick's statement here a glaring contradiction of canon.