Continuity mistake: In the scene where the witch gives Mika the dagger to kill herself with, the witch stabs it into the floor. When the witch leaves the dagger is lying on the floor. When Mika goes to grab the dagger it is stuck in the floor again. (01:15:20)
Continuity mistake: In the scene where the 47 ronin are granted a proper samurai's death, the shogun first has the black strap of his headpiece under his lip, then under his chin and then under his lip again. (01:41:00 - 01:42:40)
Plot hole: Every single one of the ronin are portrayed as being extremely lax with their most prized possession, their swords. When they first gather, one of the ronin tells Oishi "We do not have any swords", whereupon Oishi casually hand over his own. First of all, only the most poverty-stricken and desperate ronin sold their swords, as giving up one's sword was the ultimate humiliation for a samurai, it was a denial of both one's status and legacy. Secondly, selling your sword would mean never being able to be employed as samurai again, or even to be hired as a temporary bodyguard. Thirdly, swords were often inherited from one's father, or given as personal gifts by parents or lords, not something one would willingly give up. It is possible a few of the ronin would have been driven to selling or otherwise losing their swords, but not every single one of the 50+ ronin who gather. And those who still had them would be extremely loathe to even lend them to others.
Revealing mistake: When the 47 Ronin write down their names to swear fealty to the mission, they are cutting their thumbs on the swords to imprint their fingerprints on the document. The mistake is that they use the blunt edge of the sword to do this.
Factual error: In one scene, the witch Mizuki is seen observing oracle bones over a fire to do a reading for Kira. This movie is supposed to take place in feudal Japan; oracle bones are a part of ancient Chinese culture, not Japanese.