Factual error: When we see the burning 'DD' in Joe Pantoliano's glasses it is not a reflection. The DD should be backwards in his glasses.
Continuity mistake: Near the beginning of the movie we see that Matt has many visible scars on his back. But when Matt Murdock and Elektra are having sex in the bed there's a shot of Matt turning over onto his back, and almost all of the scars are gone.
Continuity mistake: When Daredevil kicks Bullseye off his motorcycle, Bullseye has nothing in his hands when he's flying through the air, but when he lands he's holding Daredevil's baton. Watch closely when Daredevil's kick connects, and you can see they never even come close enough for Bullseye to grab the baton, or for him to snatch it if it was dropped.
Other mistake: In the fight scene between Daredevil and Elektra, some of the sheets hanging to dry still have crease lines from taking them out of the package, meaning they have never been on a bed or ever laundered before, just bought for the movie and immediately hung up.
Continuity mistake: In the funeral scene, Elektra is exposed to the rain for a few moments, so that Matt can 'see' her face. She then covers up with an umbrella. When she gets in her car, her hair and face are completely dry.
Continuity mistake: When Daredevil throws his stick and it hits Bullseye on the forehead you can see a red mark where it hit, but the next time we see Bullseye he has no mark.
Continuity mistake: In the scene in the subway you see a clock counting down to the next train, at about 01:55. When we cut to the other end of the station though (instantly, because Daredevil's still coming down the stairs), the timer reads 01:35.
Factual error: When Matt Murdock is looking at Elecktra in the rain, he can make out the irises and pupils. This wouldn't be possible for two reasons. Irises and pupils have no depth that could be sensed through his radar sense. Even if they did, he could only see them if the rain was falling straight into her eyes, which would be quite painful and highly unromantic.
Factual error: When Elektra's father is killed, she picks up what appears to be a Glock 19 and empties it in the direction of Ben Affleck. We hear the weapon click a few times indicating it is out of bullets, but the slide is still in the closed forward position, and it should be locked back when it goes empty.
Continuity mistake: When Matt enters his office, his secretary is holding the invitation with 'Saturday, July 24 at 8 p.m.' on it. When Matt wakes up from his night with Elektra, however, the invitation he has reads 'Wednesday, August 13 at 7 p.m.'.
Factual error: Does anyone else find it odd that there were not only one but three window washer baskets hanging on the side of the building? How did the window washers get out of the baskets halfway up/down the building side, jump? Baskets are never left hanging on the building side because 1) it is unsightly and 2) it presents a potential for damage to the basket/building if a high wind or something comes along. They are stored on the roof top where they are secure. They are controlled from the roof or the basket to keep vandals/thieves from gaining access to the baskets.
Revealing mistake: When Bullseye stabs Elektra with her own sai, watch the profile of the sai. If you look at the angle of the piece being held against her stomach and the angle of the piece that's coming out her back, there's an obvious bend, indicating two different halves.
Continuity mistake: When Elecktra and Daredevil are fighting on the roof, Daredevil is stabbed with a sai by Elektra. After she stabs him there is blood on the window as he slides down it, yet there is no blood on the sai. The blood does not appear until Elektra holds it to his neck.
Continuity mistake: When young Matt is taking a shortcut home and he sees his father beating up a man, he runs away. While he is running, he drops his report card. When we first see him, he is riding his skateboard and not holding anything. [This scene is actually edited from a much longer scene (it is included on the 2004 Director's Cut DVD). Matt was looking for his father at a construction site near the school, and learning he wasn't there, Matt drops his report card into the puddle. This is why, later, he is shown running away with only his skateboard. Still a mistake, but there's why.]
Factual error: When DD pulls Bullseye's hands to take the sniper shot, no bullet would make a hole that fine. It would have blown his hand off, due to the force of the bullet. There was an explosion when the bullet makes first contact on his skin.