Continuity mistake: When The Bride and Hanzo are talking about her Japanese right before he serves her food, there is a shot of her laughing where she place her left hand on her right arm. When it cuts both hands are on the table. (00:45:50)
Continuity mistake: When Hatori Hanzo is talking to the bride, he calls for his assistant several times. At one point, he gets really mad and throws his knife unto the magnetic strips on the wall behind him and sticks on almost vertically. In the next few shots, the knife is positioned in different angles. (00:47:50 - 00:49:10)
Continuity mistake: When The Bride is about to pick a sword from the rack she is about to pick a sword with a red shaft. Then Hanzo says tells her to pick another one from the same rack. When it cuts we can see that the sword with the red shaft is out of sight. Later we see that particular sword is on a low level of the shaft, but when we saw The Bride reaching for it it was obvious she wasn't bending down to get it. So the sword has moved lower on the shaft by itself. (00:49:55)
Continuity mistake: During the "The Man from Okinawa" chapter, The Bride picks up a sword from one of the racks on the wall. She slides the sword out from its scabbard approx. 4 inches and stops. The next shot shows the reflection of her eyes in the blade. In the third shot, we see a wider view of The Bride again but now the scabbard is much farther out than where it used to be. (00:50:25)
Revealing mistake: When the swordmaker writes "Bill" on the window, take a close look. The window has been wiped before (as happens at the end of the scene) and "re-steamed" - you can see the outlines of the wiping from earlier takes, with a clear contrast between that pane and the others. (00:52:45)
Continuity mistake: When The Bride rubs off the name "Bill" written on the window condensation, the writing style is different from when it was first written by the sword maker. (00:52:45 - 00:53:30)
Continuity mistake: When Hattori Hanzo gives The Bride her sword, his assistant is sitting behind him in a cross-legged position. But the direction the assistant is facing keeps changing. (00:55:40)
Continuity mistake: When Hanzo hands over the sword to The Bride we can see all of her hair is hanging down on her back. When it cuts a huge lump of her fringe hangs in front of her. (00:55:55)
Continuity mistake: When Boss Tanaka breaks the bowl on the table, a piece of meatball rolls on the table. Later when the other Japanese guy throws a hand towel on Tanaka the meatball is gone. (00:59:00 - 00:59:45)
Continuity mistake: When O-Ren chops off boss Tanaka's head, the head falls in front of Sophie and another member. Then, when O-Ren finishes her speech, she holds up Tanaka's head. This can not be possible, because she has not moved from where she was standing during the speech. (01:00:20 - 01:01:30)
Continuity mistake: After cutting off Boss Tanaka's head, O-Ren whips some of the blood on her sword onto another boss' face. He jerks his head back with specks of blood on his face, but just a split second later in a different shot his head is still and there is no blood at all. (01:00:25)
Continuity mistake: After O-Ren chops off Tanaka's head at the Yakuza boss meeting, the position of her hand holding the sword changes. At first she is holding it with an overhand grip, then when the blood shower from Tanaka's neck ends, she lowers the sword and is gripping it underhand. (01:01:30)
Audio problem: When "The Bride" is cruising through downtown Tokyo, we hear the bike shift gears, but she never presses the clutch or moves the gear shift lever. (01:03:25)
Revealing mistake: When The Bride is calling out O-Ren, Sofie Fatale has her arm on the building's beam. If you look at her arm, right where The Bride is about to cut, there is a visible seam in the sleeve. (01:11:10)
Continuity mistake: When The Bride cuts Sophie's arm off you see her get covered with blood. In the next shot, however, there is considerably less blood on her top and it is in a different pattern. (01:11:20)
Continuity mistake: When O-Ren Ishi tells 'Charlie Brown' to get lost we see some blood stains on The Bride's face. The stains differ in the next few shots of her, then later when we get a close-up of her face the blood stains are the same as earlier. (01:12:00)
Continuity mistake: The Bride raises her sword twice at the beginning of the fight with Gogo. (01:14:55)
Revealing mistake: When Gogo is fighting the bride, misses and hits herself with the mace, as she falls backwards onto the table, you can see the stunt double's hairy legs. (01:16:10)
Continuity mistake: When the bride is holding a table, GoGo throws the mace ball at it. She then pulls the mace ball back through it. The table splits in two. The piece of table that falls at the bottom of the screen, the bride's right hand side, falls completely apart. The legs have broken away from the table top. In the next shot this piece of table is standing on end with the legs reattached. (01:18:55)
Continuity mistake: The table that Gogo falls on after hitting herself with the mace gets splintered into pieces, with debris underneath and all around where she lies on her back, especially in the area below her feet. Yet in the next shot when the Bride jumps down to resume her attack from above, there is no sign of the debris on the floor. (01:20:00)
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.