Interesting stuff. Its true a lot of these aren't plot holes. Just stupid mistakes made by some characters or the police force. I did wonder about the origami with Ethan though. It was never explained why Ethan was carrying those after blackouts.
And when Shelby is in the typewriter store its not a plot hole, but its missing something. I have to play that scene again to see if I missed a quick fade to black or something, but I wish it cut away from him to controlling the girl for about 20-30 seconds so there could be time to perform the actions he does.
Also for Ethan still thinking he could be the killer after the lizard. It makes sense. If you have a split personality the evil side could still be testing you and the good side wouldn't know about the other. The evil side could have just programmed the camera device to give you the next letters to the address regardless of whether you performed the action in time.