Plot hole: Sonny hides among the 1000 robots in the big store room. They are all placed in very straight rows. Sonny would not be able to take over another robot's place in the grid (when he starts running we see a large robot-sized gap) without getting another robot to move. And while Will Smith is running around the rows, he would have noticed if the others moved to make room.
Suggested correction: Sonny was already at the factory before Spooner and Calvin showed up. It's possible he moved in a robot's space, and either the robots to his sides or the ones behind him moved back a space (we never see the rows in their entirety), hence no need for any of them to move while Spooner and Calvin are in the storage room.
Suggested correction: Will Smith shot one of them, it's possible this hole in the front of the row caused that line of robots to move forward one spot, to complete the row again. As they did Sonny could have slipped in. When he spotted Sonny the first time Sonny was simply standing between 2, as Will Smith only saw them from the front at that point, when he started running it's impossible to notice a simple step forward of 1 row of robots and Sonny slipping in.
Plot hole: When Delila finds out who Jimmy really is, she takes his tuxedo and is apprehended by the bad guys. She then turns on her homing device on her necklace. The office says it will take 20 minutes to get to her. From that statement to when the CSA finally arrives, Jimmy has time to go to Devlin's, write him a letter, discover water striders, find his suit, and get back to Delila and fight the bad guys. THEN CSA shows up. The timing is really off.
Plot hole: After Nanahara and Noriko run away from Akamatsu at the school, Niida shows up from behind some bushes opposite the school and inadvertently kills Akamatsu with his crossbow. But Niida is Boy 16, which means he should still be in the school building (he's supposed to come out after Noriko, who's Girl 15). There's no way he has any time to get into those bushes.
Plot hole: When Daniel is in the air with the stolen plane from the Los Alamos air base Nat suddenly appears from behind. However, Nat had no chance to slip into the plane secretely as there was only one stepladder that had been in his mom's full view while she hugged Daniel good-bye. (01:25:30)
Plot hole: We discover that Teresa the maid has been turned into some kind of living zombie at the end of the movie. She confronts Alex and Megan near the end, and they run away from her and then fight with the Puppet Master. The issue of Teresa is then never addressed in the rest of the film, she just simply disappears from the plot and the scene. (01:13:35)
Plot hole: If the dinosaurs are so dangerous, why are they only kept behind plastic sheeting at the back of the truck, rather than in cages? There are computers in the truck, so obviously people must go in there, and it wouldn't be very safe to use computers if dinosaurs were roaming free in the trucks.
Plot hole: During the end of the film chase scene, Agent Mackelway calls Agent Kulok and gives her a vague location of where they are and asks for back up. Considering Mackelway had been kidnapped and driven out into the country, it should have taken Kulok much longer to arrive at the scene instead of the few minutes that are indicated.
Plot hole: While still unsure where and when they are, the Nimitz has two F-14 Tomcats aloft, investigating a pair of low-altitude radar contacts. They determine the planes are WWII-vintage Japanese Zeros in full military livery. The Tomcats are told to shadow the Zeros without engaging them. Then, the Captain, the XO, the CAG and Lasky all go to a formal dining room and sit down to tea. In this scene, they talk about many other 1941-era things that are happening, but nobody mentions the Zeros. That fact, and that they left their Tomcats where they did, suggests this scene was meant to be in an earlier part of the film (when things seemed odd, but no imminent threat existed) and got moved here, creating a plot hole that the USS Nimitz could slide through sideways. US Navy nuclear carrier command staff wouldn't simply go have tea under the current conditions. (00:40:30)
Plot hole: When Peyton/Darkman is showing Bridget how the liquid skin works, he drips a small amount onto his burnt finger, and it solidifies. However, when he drops it onto his finger, it magically shapes itself into a replica of a perfect, undamaged finger. This makes no sense, as it is simply a liquid and is not being molded by any forces. Hence, it should not look like a perfect finger.
Plot hole: After Riker takes the Enterprise through the Briar Patch to communicate with Starfleet he returns to rescue Picard from the collector in mere minutes, even though it was supposed to be a 2-day journey.
Plot hole: When the umbrella ops first get onto the train, rain has to power it up. There were plugs disconnected, and you see a hole in the fence as she shines a flashlight on it. It can't be anything infected because they didn't power down the red queen yet, and release the bioweapons. The red queen isn't physical, just controls systems. And with none of the zombies, or other infected loose yet, what else could have unplugged it? Spence was knocked out on the train, this seems to be a plot hole. (00:02:00 - 00:20:10)
Plot hole: In the scene where Ba'al goes through the stargate and arrives in 1939, the event horizon from the stargate puts a hole in the haul of the ship. Later when SG1 goes through the stargate the hole is covered with ice. The event horizon created from SG1 would have been the same as the previous one and removed the ice from the hole.
Plot hole: Lois and a friend of hers are watching Non and Superman fight. But this is totally senseless, because Superman had been flying around Metropolis and chances are slim that he appears in the very same spot to let Lois watch him. And, second and most important, should any doubts arise, the panning angles of the camera never show Lois's building, with the big broken window and the flag poles.
Plot hole: When the asteroid first approaches Earth it does so very quickly, but then it takes hours to finally enter the atmosphere and land on Susan.
Plot hole: Gerry's wife uses a rocket boot to break through a window and then slides down a curved wall to get to their son. She does so gracefully and takes off running. Gerry slides and takes a hard tumble and rolls down, landing on the ground. The next shot shows Gerry running behind his wife and not too far away as they reach their son. Even if it was to show a little time passing, there was not enough distance between where they broke the window and their son for Gerry to have picked himself up and catch up to his wife before reaching their son, especially with his wife being a worried mom doing a full on sprint to her kid.
Plot hole: The helmet design is rubbish. The eyeholes are far too small - that close to the eyes the divider between the eyeholes would block almost a third of the wearer's vision. He would hardly be able to see what was right in front of him - and it is not too close nor too narrow to fall into the "blind spot" between the eyes. This is not a character error by Peevey - the helmet design came from the original plans - it is even shown in the German propaganda film!
Plot hole: Near the end of the film, the crippled Thunderbird 5 is about to catastrophically re-enter the Earth's atmosphere and burn up. Predictably, the younger Tracy brother restores control, saves Thunderbird 5 and all on board. A few seconds later, a computer announces that Thunderbird 5 has resumed a geostationary orbit (such orbits are only possible at an altitude of 400km) My point? Pulling out of a fall, climbing 370km in a few seconds, and then stopping dead 400km up would have required such a massive acceleration/deceleration that everyone on board would probably have been pulverized, even if it were possible for a badly-damaged space station to move that fast.
Plot hole: During the nova scene, everyone is tying down the sails after securing themselves with lifelines to the mast. Jim and Silver are on the front and Silver is knocked off. Jim is then all dramatic and runs to grab Silver's lifeline which seems to be coming from above, and pulls Silver up like a pulley. How come? The lifelines were attached to the mast, so Jim's action is pointless... even if he could do it, because a shot later both lifelines are streaming right to the mast, leaving no room for a pulley of any sort.
Plot hole: The giant-sized teenagers show themselves at the garden party and start making threats about taking over the town. They then spend the night in the theatre, and the next day they decide to cut off all communications to and from the town. For some reason, not one of the party-goers, or the sheriff, decided to call someone during the night and tell the remarkable story about 30 feet tall teenagers seizing the power through force.