Plot hole: The Tomahawk Cruise Missiles the Arleigh-Burke Class destroyers carry have a range of approximately 1500km. As soon as Alex got the message from Sam, they could have blown that Saddle Ridge communications facility to kingdom come with just a few cruise missiles. They didn't need to get in range because the entire dome surrounding the Hawaiian Islands was smaller in diameter than the range of the Tomahawk Cruise Missiles. Cruise missiles have internal guidance, so they wouldn't rely on the radar, which was jammed.
Plot hole: As the island is sinking you can see parts break off, like the island is falling apart, but if it does this every 70 years then there wouldn't be an island. It should have completely fallen apart hundreds of years ago.
Plot hole: When (future) Agent J and (future) Boris are fighting on top of the large red docking station for the spaceship, Agent J gets shot deliberately by Boris and jumps off the edge of the dock. Then he uses his time travel device to go back in time a few seconds earlier to be able to dodge the shots. There are a few mistakes in this part. 1) There should be another Agent J and Boris there too, as they have gone back in time to that moment again. However in the movie there are only two of them. 2) The injuries sustained by Agent J (the bone spikes in his abdomen) should have remained there when he went back in time. If it were true that you healed once you went back in time into the condition you were in at that moment, then Boris should have grown an arm back when he went back in time. 3) Due to the time loop, Agent J remembers how to dodge the shots, while Boris doesn't remember anything and is surprised by the outcome. (01:29:00 - 01:30:10)
Plot hole: Hock sneaks a gun into the prisoner interrogation area because he is told that guns are not allowed there. If the prison was so strict about keeping guns out of that area then they would surely have metal detectors to prevent such a thing from happening. (00:15:25)
Suggested correction: Not a plot hole at all. Most of the people who are allowed in those areas will be government employees, who will be deemed trusted enough to follow the rules.
Plot hole: The killer has been living in the (apparently big enough) crawlspace between walls and floors, for over a decade. There is no explanation (or rationale) given on how he moved the various objects inside every room, closed doors, fed when the house was not occupied, hid the various corpses and, silly detail, concealed his own BO and the stench of his own living quarters, which is something hinted at when they find out his hideout. It is explicitly said that he is agoraphobic and does not get out, ever.
Plot hole: In this Australian time-travel fantasy, a college student discovers a one-way time portal that allows him to travel one day into the past each time he uses it. While he at first attempts to rescue his girlfriend from a traffic accident that occurred a day earlier, he eventually travels back 50 years (one day at a time) to save his young grandfather. However, in order to go back 50 years (one day at a time), he'd have to repeatedly climb through the portal over 18,000 times. Apparently, it's not an issue, because the movie just glosses right over it in less than a minute.