During moments of the samurai's last cavalry charge into the infantry line, Colonel Bagley can be seen without injury after his supposed earlier impalement with the sword thrown by Algren.
When Katsumoto is in the courtyard discussing poetry and perfect blossoms, he has a cut on his forehead from the ninja attack. He announces that they will be departing the next morning, but when we see him the next morning, the cut has completely healed.
When the ninja invade Katsumoto's village, a ninja is shown quietly killing a samurai sentry by snapping his neck. Later, just before the final battle, the same samurai is ready for battle and staring the enemy army down.
When Algren is fighting off multiple samurai attackers, not only is there no blood on the sand, though a bloody battle has taken place and Algren has been severely wounded by a spear more than once, there is also no blood on his uniform. The only sign of his wound is a cut in the otherwise bloodless cloth of his jacket, visible as the band enters the village.
When Nathan walks into Taka's house after his first round about town since his capture, Taka cleans up after him because he has walked in with muddy shoes. The shot before this showing him walking in the door clearly shows clean shoes.
Japan *did* seek military advisors in the latter half of the 1800s to form a modern Army. The only problem with this is that they didn't consult the Americans to assist them. The most successful army at that point was the Prussian (not yet German) Army, whom they recruited for training purposes... as well as British naval attachés to assist in the creation of a modern fleet (which thoroughly embarrassed the Russians at the Battle of Tsushima in 1905 and established Japan as a fledgling world naval power).
Katsumoto (as leader most especially) would have had his hair style in the 'top-knot' fashion, as would all of his samurai. To have it any other way was unthinkable.
In the final battle, the cannons are firing from across the field. The cannon is heard at the same instant as smoke is emitted from the cannon. In reality, at that distance, the smoke would be seen first, followed by the sound of the cannon shot a second or two later.
In the opening scene when Captain Algren is being introduced as a hero of the Union Army, the music being played is "The Bonnie Blue Flag" which was a Confederate marching song. Hardly the music one would play for a Union hero.
When Algren and Katsumoto are shown in slow-motion, during the horseback charge, Algren draws his sword with the sound of the sword ringing as it is drawn. The Saya (scabbard) of the Katana is typically made of wood, and though they sometimes had fittings made of metal around the Koiguchi (mouth of the scabbard), these were usually ornate, and there clearly are none on the sword that Algren has.
The armor the samurai wear is from the mid- to late-Sengoku Jidai era in Japan, over 250 years before the Meiji Jidai era the film takes place in. This was deliberate: costume creators were aware that no armor would have been worn at the time the movie takes place, but they chose to have them in armor to show that the band of samurai wanted to go back to old values and rejected modernity.
At the final battle Algren tells Katsomoto about the battle at Thermopylae, and says that 300 brave Greeks held off an army of 1 million Persians. This is only partially true; there were 300 Spartans, but the Persian invasion force is believed to have had 150,000 soldiers. Of course, stories from ancient times describe the brave Spartans as heroes who stood up against 1 million Persians, and at the time of the movie it might still have been thought so. In addition, while the 300 were killed by the Persians (as they knew would happen), their stand inspired the Greek states to rally against, go to war versus, and eventually prevent an attempted Persian conquest of Europe. It's not unreasonable for Algren to describe the Spartan stand as a victory, not least because of the parallels between what happened at Thermopylae and the samurai's willingness to die in service of the Emperor - along with the fact that Katsumoto's stand does result in posthumous victories (the American treaty is rejected and the Emperor angrily confiscates Omura's entire fortune).
The horse ridden by Captain Algren as he enters Tokyo with the Samurai band is not the same horse he was mounted on as they leave the village (the distinguishing mark on its forehead gives it away). Katsumoto's mount at this point is not the one he is astride in the rest of the film, either.
(Horses were often swapped during travel to keep them fresh. The distance ridden is not stated, so arriving on a different horse wouldn't necessarily be wrong.)
When Algren Tom Cruise fights Higen in the rain, the bokken or wooden swords used are much too long for either child. The Nihonto (Japanese Sword) was made to correspond to its users height and arm length, this being measured by holding the sword in the dominant hand and letting it hang at the bearer's side. The tip of the sword should be just an inch or so short of the ground. However, it seems this "mistake" was deliberate as Algren would NOT have been able to fight with a sword that was the length either boy would be using.
When they are disembarking the ship in Japan, the green screen spill on the side of the ship and a hole through the ship reveals the CG water behind.
In the final battle, one soldier takes an arrow directly in the face. But the actor's hand is already held up to his face, palm inward, before the arrow arrives.
When Katsumoto, Algren and the rest of the Samurai are charging on horses towards Colonel Bagley and the infantry in the final battle, Katsumoto is shown with a bullet hole in his shoulder armor and moments later he is shot in the exact spot. The bullet hole was there before he was shot.
The Gatling guns used brass ammunition, yet expended shell casings are not ejected in some scenes.
The samurai never considered using firearms to be "dishonorable." In fact, they had been using guns and cannons ever since Portuguese traders first brought them to Japan during the 16th Century, still used firearms during the Satsuma Rebellion, the war that this movie is based on.
The Meiji Emperor would not have been called by that name until after his death. Meiji was his "nengo", or reign name, and that name for Japanese emperors is only used after their death; e.g. the Emperor Hirohito is now known as the Showa Emperor, Meiji's name was Mutsuhito, and he was referred to as Emperor Mutsuhito during his lifetime.
General Omura Masujiro who developed the Western-style army during the Meiji restoration was killed in 1869 by a conservative samurai, several years before the movie takes place.
There is a modern telephone pole in the village.
During the final battle sequence, modern equipment is visible on several occasions when the Gatling guns begin firing (and continue to be fired). The equipment is clearly visible in the distance over the shoulder of the soldier cranking the Gatling gun.
When Captain Captain Algren arrives to Japan at the port of Yokohama, he is taken by Mr. Graham in a rickshaw to the see the Emperor immediately, and the palace is even seen in the panoramic shots of the city. However, the Imperial Palace is located in Kyoto, almost 500 km. away from Yokohama.
When planning the last battle, Algren advises Katsumoto to 'take away the advantage of their artillery'. He then lines his men up in a beautifully tended grassy-bowl of a battle field, directly in front of the enemy artillery, making them easy targets, and wastes a lot of lives before eventually having his men appear to retreat. Had he arranged his men behind cover the artillery would have been useless and the enemy would have had to advance anyway.
When the Ninja attack Katsumoto during the NOH play, Algren shouts a warning, but Katsumoto freezes in place, looking at the roof and making himself an easy target. He is lucky that the crossbow bolt strikes the mask-wearing actor beside him. Algren's warning makes no difference to the attack, or the initial result.
After Katsumoto and Algren meet with Colonel Bagley and Omura before the final battle, Algren rides back into the Samurai front lines. When he dismounts his horse, the horse kicks back and hits one of the Samurai who then stumbles backwards unsure of what just happened.
No one, especially a foreigner, would have been allowed in the Emperor's presence bearing weapons, yet this happens on three occasions.
Colonel Bagley mentions that the new Gatling guns possessed by the Japanese Imperial Army are capable of firing 200 rounds per minute. Unless the "new" guns are very early versions of the Gatling gun (this is not what is shown), his statement is incorrect. By the 1870s Gatling guns had a rate of fire of at least 800 rounds per minute and, depending on the specific model, significantly higher rates.
At the beginning of the film, the narrator says a "sword" was dipped into the sea and the four islands of Japan were formed. This is factually incorrect; it was actually a jewelled spear, called Ame no nuhoko and is detailed in the Kojiki, the book of the Shinto faith.
When Algren and Simon go to rescue Katsumoto, one of the guards on his door is the same solider who attacked Nobutada in the street. He should have recognized Algren and sounded the alarm.