Plot Hole 1
(SPOILER)If you make sure that Madison survives to the hospital scene near the end, she (but not you) is told the identity of the Origami Killer. Understandably, she is shocked and aghast at the name she hears being associated with such atrocities. Not understandably, she and said killer have never met in the game at this point, and in fact are completely unaware of each other’s existence. She’s reacting to nothing, which becomes even more face-palm-worthy when she scoots immediately round to his house.Explanation
(SPOILER)
She's an investigative journalist. It's not unrealistic to think she may have been aware of a former high ranking police official who makes his work as a PI.
Plot Hole 2
Explanation(SPOILER)While investigating the Origami Killer, private eye Shelby interviews several parents of murdered kids and collects key evidence and messages sent to them by said mysterious child-offer. Question: Why the hell have these parents still got hold of this stuff? Why didn’t give they these clues to the police during the investigations? Did they want their kids to be killed? And if they did hand them in, why haven’t the police still got them in the (still open) case file? Did they give them back as souvenirs when the bodies were found? No wonder they can't catch the killer if they keep giving evidence away.
(SPOILER)Or, like Ethan, some of these people may not have turned everything over to the cops immediately. Sure, that's a stupid move, but obviously people make stupid moves. Emily's mother mentioned her father leaving shortly after their son disappeared. The father could have left attempting trials, given up and bailed (or even died trying).
Plot Hole 4
Explanation(SPOILER)Speaking of manhunts, the whole case against Ethan which takes up much of the second half is a farce. The evidence that makes him the definite, absolute, couldn’t-be-anyone-else, number-one suspect in a high-profile murder case? Nothing more than some highly circumstantial hearsay and tittle-tattle about black-outs and bad dreams, from his ex and his psychiatrist (tittle-tattle that in that latter case has to be beaten out of the unwilling source). We know that the cops are looking for a scapegoat, but making public claims of guilt and holding a press conference to celebrate the capture of a notorious serial killer without ever bothering to build any kind of a case against him is the simplistic and lazy thinking of a nine-year old. Even bad movie cops wouldn’t do that.
(SPOILER)Perhaps it's cliche, but I don't think Blake gives a sh*t who he gets. He wants to get someone and say he solved the case. Flimsy evidence or not, he wants a scapegoat. Sure this is a lazy trope trotted out in all types of action movies, but far from a significant plot hole.
Plot Hole 5
(SPOILER)
Ethan’s blackouts can be explained as a sympton of the trauma he suffered when hit by the car, but what’s with all the false-lead origami models he keeps waking up with? Was the killer following him 24/7 the whole time with a copy of his medical history, just waiting to pop one in his hand whenever he dropped? Including that time he passed out in his own house?
Does he really have an undiagnosed case of ‘Making-paper-models-in-your-sleep-at-topically-suspicious-times’ syndrome? It’s as sensible an explanation as any.
Explanation
(SPOILER)Shelby made it clear in the ending that he had been paying attention to Ethan. While it might seem far fetched, he seemed to have an extra keen interest in Ethan and very well may have spent sometime placing those figures in Ethan's hand. Far out there, but not that bad.
Tired of typing... maybe more later.