Plot hole: When Ward's son hits the switch marked "Do Not Touch This Switch", every light in the amusement park comes on, music starts playing, and the rides all start moving. It's a funny gag, but it seems unlikely that one switch would power every single thing in the amusement park, and that everything in the park has been left on "full speed." If that's the case, when Angelo first sent the two lookouts to the top of the ferris wheel, everything else in the park should have come on then too.
Plot hole: When the police search the white car and the barn they fail to find the compartment in the car behind the boot in which the decoding equipment was hidden. This is completely improbable. It was a standard car, the compartment was not a secret add on, and the police were supposed to undertake a thorough search of everything.
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: Roger's initial briefing at the beginning of the film states that 'Tom' goes out from 104 and 'Harry' from 105. Despite this the goons are said to be in 105 when they find the entrance to Tom.
Plot hole: When the Allies blow up the airfield they pour gunfire from the backs of the trucks into the tents where the Japanese soldiers are eating. If you watch carefully you will see that the Allied guys in the truck nearest the screen are pouring lead through their comrades in the other truck. Another classic case of 'friendly fire'.
Plot hole: When Archie and the others take the castle acting as Saddam and his guard two Iraqi soldiers come running out, passing by Archie and Chief, for some reason not looking at them and thus not noticing their American uniforms. (01:18:55)
Plot hole: In the scene where William takes Murron for their initial ride, he shows up in pouring rain, yet all further shots show the two of them totally dry. The tone of her mother's voice when they get back suggests they did not spend the night together, and the whole sequence appeared in a couple hours. They could not have gone from soaking-wet to bone-dry that fast.
Plot hole: In the scene where Colby is discussing tactics with the team, Pele interrupts and takes the chalk from Colby and says "Hatch gives me the ball here, I do this, this, this, this, goal" while drawing a line on the blackboard to indicate dribbling from one end of the pitch to the other. At that point in the film, Hatch was only the trainer, not the goalkeeper.
Plot hole: The police wanted to take Julian's father away as a Jew because they found out his grandparents (plural) were Jewish. Even assuming they were only talking about one set of grandparents, this would make the father half Jewish, and therefore in the eyes of the Nazis, a Jew. That means that Julian would then be one quarter Jewish, and also considered a Jew. But the police then go on to say that the father is one quarter Jewish, but Julian is only one eighth Jewish, and therefore not a Jew. But he'd have to have only one Jewish great-grandparent to be non-Jewish, and they already confirmed that he had at least two. The numbers don't add up.
Plot hole: "The regiment headquarters calling for Corporal Steiner. Come in Steiner." The film starts with this repeating radio message. It's even heard by Steiner and his men who are on their hush-hush job behind the enemy lines: a reconnaissance mission. Calling Steiner just makes no sense, especially with the name.
Plot hole: The whole basis for replacing Admiral Broderick with John Wayne as operational commander of Sky Hook was that Admiral Broderick was deemed a failure. Wayne took over, planned for what looks like a week or so and launched an attack. First point - the Japanese had evacuated the island. It's pretty hard to miss the evacuation of 15 or 20 thousand soldiers by the IJN which would have made multiple large sorties over a period of several days. Also, there would have been massive explosions and fires as the Japanese destroyed facilities and supplies rather than leave them behind. (Check out the real evacuation of Guadalcanal during WWII - the IJN operation was so big we thought they were reinforcing the island) Second point - seems like Admiral Broderick's approach, no matter how incompetent it looked, must have worked. The Japanese gave up and left and it must have been as a result of Broderick's efforts. An evacuation like this takes time to plan and time to execute. The evacuation was decided upon prior to Wayne's arrival (Broderick had already won) and took place right under his nose (complete reconnaissance failure by Wayne).
Plot hole: Danny receives the telegram from Rafe, telling him that he is alive, at the same time Rafe meets with Evelyn. The telegram must have been sent from Hawaii. Why didn't he just call on the phone? When Rafe reached the U.S. after leaving England why didn't he send a telegram then. In those days it took some time to travel from the Eastern U.S. all the way to Hawaii and there is no way he beat the telegram if it was sent when he returned to the U.S.
Plot hole: When Bo-Tat is purchased the Village Elder insists that Lihn go with Bo-Tat, it is CLEARLY established at this time that A) Lihn is an orphan and B) his parents were both killed in the war. For two-thirds of the movie Capt. Doyle repeatedly comments that Lihn can't be trusted because we don't know who (NVA or USA) killed his parents. There is no possible way that Spc.5 Farley wouldn't know this. However, halfway through the movie (on the river boat) he asks Lihn where his parents are and how they died. He couldn't possibly be ignorant of this, since he took part in at least two of the prior conversations.
Plot hole: When Hornblower arrives home from the Pacific, he meets his son, a baby in a cradle. He is given the Sutherland, sails to Spain, is captured and escapes, and returns to England a hero..all in under a year. However, upon arriving in Portsmouth to see the Admiral, he visits his son, now a child of 3 or 4.
Plot hole: When Nameless and Flying Snow are fending off the arrows, the arrows blocked by the two seem to be the only arrows coming toward the school, as there are no arrows flying beyond their reach (omitting the ones missing the school entirely).
Plot hole: Towards the end of the film when Private Shakespeare is talking to the wounded soldier, his coat and hair are suddenly dry, strange when the majority of the film is set outdoors in the rain.