Deliberate mistake: When the Crazy 88 crew is coming in to attack the bride they use one of the shots twice. It is the one that shows 1 guy jump over a banister and go to the left of the screen then another guy comes directly after him and heads directly towards the camera. It happens at 1:21:49 and 1:21:53. (01:21:45)
Continuity mistake: During the fight in the restaurant, the Bride is surrounded by a large group of Yakuza. In a shot from behind her, she is staring at the opponents in front of her over the edge of her horizontally held blade. One of the masked villains is swinging a chain in an arc. A moment later the shot cuts to an overhead and the guy with the chain has disappeared - everyone in front of the bride (as well as to the rear and sides) are holding swords. (01:22:30)
Revealing mistake: When the Bride is fighting the General of the Crazy 88's he slashes at her lower torso and scores a hit, but the slash on the Bride's jacket is already there before he strikes (it is not there in the previous scenes and when he slashes it makes the sound of him cutting the material). (01:23:10)
Revealing mistake: During the restaurant fight scene, Thurman's fight double can be easily spotted from time to time as she is a few inches shorter and a little heavier than the star. It is especially noticable during the silhouette sequece. (01:23:30)
Continuity mistake: When The Bride is fighting the Crazy 88s, right after it changes from black/white screen to color again, they fight in a room where the light gets shut off. Now watch close, they wait. They fight. She hits a few members of the gang. Watch the gangster in the lower left corner of your screen. He's gone. He rolls away to the left. They start fighting again. Keep paying attention to the lower left corner. You see him roll away again a few seconds later. (01:27:25)
Continuity mistake: This error only occurs in the Japan version: Here, the little boy (the only one who doesn't wear a mask) "The Bride" fights before confronting the head general of the Crazy 88 had already fought against her in the middle of the battle with the rest of the gang. In that short fight she cut his mask off (explanation why he doesn't wear it at the end), realised he was only a child and then instead of killing him threw him into one of the pools. You actually see him falling into the water. But at the end when they meet again, he is completely dry (except for his sweat). (01:28:35)
Continuity mistake: When The Bride is slashed on the upper back by O-Ren in their fight scene she collapses and lands on her back in the snow. After she gets up and the fight continues, there is no blood spot on the snow where she was lying. (01:29:55 - 01:31:10)
Continuity mistake: When O-Ren takes off her sandals to fight the bride she pushes her right sandal out from under her. It slides on top of the snow and does not push around a lot of snow. No snow collects around it. In the next shot when she takes off her left sandal, the right sandal now has a lot of snow that was pushed up around the side of the sandal and collected beside it. It is also sunk much deeper into the snow than in the previous shot. (01:31:35)
Continuity mistake: At the beginning of the fight between Oren and the Bride in the garden, Oren puts the sword up to eye level and starts to withdraw the blade from the scabbard. The shot switches to a view from behind her and we see the back of her head. The eye-level sword, however, is nowhere to be seen. When the shot switches back to Oren's face, the sword has reappeared. (01:32:20)
Continuity mistake: When O-Ren falls dead in the snow, only the snow by her feet is pushed up. In the next overhead shot there are big footprints/marks in the snow near her legs, and her samurai sword has also moved. (01:33:35)
Continuity mistake: As The Bride writes her "Death List Five" on the plane, the handwriting of everything greatly changes between shots. (01:38:15)
Continuity mistake: When The Bride gets into the Pussy Wagon and tries to move her toes, the shot changes between one taken from her head and one taken from her feet. The one taken from her head shows her two feet touching one another and resting against the closed door. The one taken from her feet (which would have necessitated the door being open) shows her two feet not resting on anything and slightly apart from one another.
Continuity mistake: When we see the Bride in the "House of Blue Leaves", her hair is considerably longer than when it was while she was walking through the Tokyo airport. Since we see from time to time in the movie, the notations "one month later," or "4 years later," and there was nothing like that in the sequence, it seems that the Brides' hair grew at least 4 inches from the time she left the airport until the time she gets to the restaurant.
Continuity mistake: When Vernita and The Bride are talking in the kitchen and Vernita shoots The Bride from the cereal box, you can see the bullet hole in the back wall of the kitchen, but then a little later that part of the wall doesn't have any bullet holes. Also, not only is the bullet hole not where you see it hit in the first place, it's on the other side of the bride's head, along with the splatter from the cereal box.
Factual error: When we see the closeup of the gun when Bill shoots "The Bride" it is obvious that it is a normal gun with rifling in the barrel, we even see the end of the grooves when the bullet comes straight out of the gun at the camera, but the bullet does not spin.
Other mistake: The Japanese phrase the chef says to The Bride when handing her the food is used after a meal, not before the meal.
Continuity mistake: During O-Ren's speech the blood on her forehead changes between shots.
Continuity mistake: When O-Ren Ishii beheads Boss Tanaka, the bald boss sitting next to Tanaka alternates between holding a fan and not. After Tanaka's head is chopped off, there's a quick shot to bald boss to see his reaction, and he's holding a fan. When the shot goes back to him a second time, the fan is gone.
Continuity mistake: During the restaurant fight scene to get O-Ren, the blood on The Bride's face (particularly her nose) keeps changing. This may be an homage to older martial arts films, but at one point towards the end it is in the same spots as it was in the beginning as well.
Continuity mistake: When Gogo gets hit by her metal ball, she falls and breaks a table, and a lot of splinters gather around her head. In the next angle, for only a couple of frames, there are fewer splinters.
Answer: From what I understand the reason for the lights being off is the same reason for why the previous scene was done in black and white; to decrease the amount of 'graphic violence' in the movie in an attempt to keep an 'R' rating. I would assume that they had him shut off the lights for that scene as just another method to accomplish that task.
I believe the original question was asking why was it done within the context of the film (i.e. why did the character shut off the lights) not why was it done in reality. My best guess is that the manager switched off the lights thinking the 88 had a better chance of killing the bride if she couldn't see. True, they couldn't see either but there were so many of them one could possibly have gotten to her.