Mika is awoken by the witch and told that Kai has been killed. The witch sticks a knife into the floorboard beside Mika's head. It is shown from different angles, however, when the witch is leaving the room, the knife is lying on a pillow. In the next shot, the knife is once again stuck in the floorboard.
When Oishi and Kai are escaping the Dutch Island. Right after the battle Oishi's sword vanishes and only reappears in his hand after he and Kai fall from the higher pier to the lower one.
Near the end of the film, during Mika's elaborate, large-scale wedding to Lord Kira, she is shown in an all white wedding kimono ensemble. In contrast, traditional Japanese wedding kimono colors are red or another rich color, such as purple or turquoise/teal. The only traditional Japanese wedding where the kimono is white (symbolizing purity) are Shinto weddings, which are small, private affairs, just family and close friends.
Keanu Reeves character may not be pure blooded Japanese but still was raised there. So it makes no sense for him to mount the horse from the LEFT as is the North American custom when in Japan, one mounts from the RIGHT.
The Dutch flag in the harbor looks like it is hanging upside down. The flag is down. Rope to raise it can be attached to the red stripe side as it seems to be on the stern, as most of the fluyts (dutch cargo ships) did.
When Mika visits Kai in his hut (after battling the monster), she is shown walking through the rain with a parasol. When she leaves, she uses the hood of her cape to protect her head, and the parasol has disappeared. (The parasol is outside the door and she can be seen reaching down for it.)
In several of the scenes, it is highly noticeable that the flags and banners and tents used throughout the movie are machine stitched with modern double needle stitching. Also that the loops used to attached to poles are stitched in the "X in a box" style not used till very recently in history. For a clear example see (time-stamp)21m0s when the Samurai challenger in the silver mask and suit emerges from the tent and look at the banner in the background. The mechanical sewing machine will not have been invented for at least another 50 years after this historic incident had happened. and the sewing machine still would not reach Japan for many more decades.
The black horse that Kira rides is a Friesian which is not native to Japan.