SO MANY PLOT HOLES

About your last plot hole: the caption in the newspaper says "Local man Keller Dover has been missing since yesterday". So he wasn't missing for two weeks and very likely would have been alive when Loki heard the whistle. A couple other things were stretches though.

I'm gonna tear your "plot holes" apart now, so suit up and especially pay attention to 6, cause the rest are not plot holes, but just your opinion. Stretches are not plot holes. Plot holes are something that contradict the plot, stretches don't contradict anything. Whereas you are dead wrong about point 6. (the red whistle and Dover's missing), which could actually have been plot holes, had you not been wrong about them, as I'll go on to explain in 6.:

1. We've just had an example here in Denmark where I live about a priest who got arrested for pedophilia and need I mention the various cases of catholic priests around the world. The reason he killed Holly Jones husband was because she and her husband would rage war on God. She say's that to Dover in the end of the movie that that was their plan and her husband had confessed that to the priest and confessed he'd killed 16 children. The priest could have therefore killed mr. Jones because of religious beliefs or try to "make up" for his own sins.
Things being a stretch from the ordinary does not make a plot hole. A plot hole is something that contradicts a plot/story, hence why it's called a plot hole.

2. He probably didn't report it out of fear of the consequences or it could have been due to brainwashing. There's many time where an abducted does not report the incident or a raped person does not report the rape, etc. Nothing stretched or plot hole about that. Bobby Taylor was obviously still obsessed by what happened to him, hence the maze drawings constantly and all over his walls plus he looked to still be heavily brainwashed.

3. Still not a plot hole. People has various reasons do what they do. Some even don't have any it seems. I think their reason was explainable due to them being angry on "god" for taking their son and thus wanted others to feel the same pain. That's not a stretch, that's something we unfortunately do see. Holly Jones even mentions that she and her husband where religious before the death of their son.

4. They killed the 16 children according to the priest. It's not that easy to track murders back if there aren't much clues or evidence to backtrack them. Look up serial killers and how many murders they get away with before they eventually makes mistakes and get caught...Hey, just like Holly Jones, eh.

5. Alex Jones was the first child they abducted and was brainwashed. Holly and her husband used the brainwashed Alex to attract and captive more children for them. If you're brainwashed to the point of not remembering any much else beside a maze, nothing and no violent harm upon you is going to make you confess anything.

6. Grace Dover does not conveniently mention the whistle to Loki at the hospital. Anna and Joy goes missing, because they go to Anna's house to look for her red whistle. She asks her mother (Grace) if it's okay they go search for it. Later when Loki visit the Dover's, Keller comes in and say's the children where looking for Anna's whistle and Loki replies that he's aware cause he's read Keller and Grace's statements to the police. Then later at the hospital when Anna is found, she, Grace, Joy and Joy's mother go visit Loki's hospital bed. Anna has the whistle around her neck, Loki notice this and say to Grace "So she found her whistle?" in which Grace replies no, they bought her a new one although Anna insists to Grace that Joy helped her find her whistle before they were taken, hence why they had the whistle with them down in the hole and Keller later finds it. So yeah, Grace did not conveniently mention the whistle to Loki. Loki noticed it and brought it up.

You're also wrong about Keller being missing for two weeks. The newspaper says right under a picture of Keller Dover "Local man - Keller Dover (above) has been missing since YESTERDAY! Remember that Holly Jones said that Dover would probably have 24 hours left due to his bleeding, that's why he only have the power to whistle out air in the whistle.
You'd actually also realize it hasn't been two weeks (I don't know where you even got that from?) if you looked at Loki's head which still has blood under and around the bandage. Had he been in the hospital for two weeks, there probably wouldn't have been wounds with fresh blood. But the newspaper is a dead giveaway, so you don't need the other reason as to why you're wrong.

My advise to you, would be to go back and watch the movie, then perhaps come back with some actual plot holes. The only real things that could have been plot holes were The whistle part and Dover's missing, but they are not plot holes, cause what you believe to have seen is simply not correct.

So there you go. It took some time to respond, and english is not my native language, but I felt I needed to make a response, because the word plot hole gets thrown around a lot these days and it makes me fear movie makers will become afraid to actually make clever movies, cause audiences can't follow the plot. I don't need another Fast Furious movie. I need more Prisoners movies.

Over n out.

Yeah, the plot stretched plausiblity more than once.
But a plot stretch is not a plot hole. A plot hole is when the movie is inconsistent within itself. Everything here ties together, no matter how unlikely it appears.