Continuity: In the final fight between Neo and Smith, when Smith throws Neo inside a building, he flies inside the building through the hole. When Smith is inside, his flight causes a lot of dust. In subsequent shots, the dust has settled in only a few seconds.

Continuity: When the Logos plummets from the sky and crashes into the machine tower, Trinity is skewered with cables. In slo-mo you can see that at least two cables penetrate her upper chest, but when Neo is lying next to her a minute later the cables have impaled her below the ribcage and there are no chest wounds.

Visible crew/equipment: When Neo wakes up in the train station, Sati's dad tells her to, "Leave the poor man in peace." When she runs off, a piece of tape is visible at her feet, showing her where to stand. This is visible in many wide shots, but particularly in this shot.

Continuity: After Neo has been blinded, his eyes and everything around them is burned and red. Right after the fight, when Trinity sees him blind for the first time, his eyes (or eyelids) are grey, and only the rest is red.