In the closing moments of the final battle, the bandits fire two musket shots only seconds apart. It is clear from the plot that at that point they possess only one musket. The black powder muskets of the age required much more time to reload. This error was pointed out in the commentary of the deluxe DVD edition.
Shichiroji throws a spear out the door of Rikichi's hut in anger, it lands obviously in parallel with the door. Later, after Kikuchiyo's outburst he runs outside and picks the spear up, however it's now laying sideways compared to the door.
When the samurai are giving battle advice to the peasants, who sit around them forming a circle, the camera does a rather wide circle shot of them. You can see the dolly track behind the seated peasants.
At one point in the English translation of the Criterion edition, one of the characters makes reference to "playing possum," Opossums are only found in the Western Hemisphere, and would have been unknown to medieval Japan except possibly by a few scholars.
The goof items below may give away important plot points.
When Heihachi (the first samurai to be killed) is shot, the rifle shot is heard after he staggers and starts falling down. Also, when the bandit chief shoots deserters, the rifle shot is heard after the second bandit is hit and starts to fall from his horse.
During the final battle, when first we see Kikuchiyo enter the females' hut, it appears that he backs the bandit out twice. In reality, it is two different bandits, as can be seen by the fact that they are wearing different helmets. What is strange is that Kikuchiyo kills the bandit chief, who fired the two final and fatal shots, but the second man (wearing a kabuto with a wide, flat neck-guard) seems to vanish without trace after leaving the building.