In the initial fight scene, The Samurai cuts the first two adversaries in the mid-section, then slices the last man's arm off. That last man is first seen from behind holding the sword in his right arm above his head, but the arm holding the sword shown moments later is a left arm.
When Sanjuro practices throwing the knife at a leaf, the wire on the knife is clearly visible (the scene was filmed backwards; the knife was actually pulled off the leaf by the wire).
The interval between the noise of the gunshot and the ringing of bell is too long.
The 2:00 AM meeting between the gangs was clearly filmed in broad daylight.
The wire used to pull the Yakuza's cut kimono off can be seen as he gets up from the ground.
When Sanjuro smites his opponent's arm off, the arm can be seen moving under the poncho.