Plot hole: When Buffy talks to Xander at the end and he tells her to stay with Riley, she mentions that he is going at midnight. But earlier in the episode, Riley doesn't tell Buffy he is going at midnight, he says "Transport's leaving tonight" first, and at the end of the conversation he says "Unless you give me a reason to stay, I'm leaving tonight". Nowhere in this episode does he tell Buffy that he's leaving at midnight.
Revealing mistake: When Buffy is fighting the vampires that are trying to resurrect The Master, at one point she is grabbed from behind by a male vampire and kicks a female vampire in a green top twice (right after Absalom shouts "The sacrifices! Stop them!"). If you watch closely, both of the kicks miss the vampire, revealing that the fight was choreographed. The punch that she delivers to the male vampire afterwards also looks fake.
Continuity mistake: When Buffy and Spike are fighting on campus during the day, Xander tries to help Buffy but Spike throws him against a lamppost. When he lands in the ground he falls completely on the grass on his side but if you look behind Spike in the next shot he lies half on and half on the grass on his front.
Continuity mistake: In 'Consequences' Buffy says to Faith 'Less that 24 hours ago you killed a man'. In 'Bad Girls', Faith kills Finch in the alley on the first night. One night later Buffy and Angel are attacking Belthazor, the night after that is the night when Buffy dreams about drowning, so the night when Buffy says this is actually about 72 hours after the murder.
Audio problem: In the episode 'Once More, With Feeling', when Anya sings her first few lines of the song 'I'll Never Tell', you can still hear Xander talking about omelettes in the background, but for the last few lines he speaks (from 'I could do an omelette' onwards) you can see over her shoulder that his voice is dubbed.
Revealing mistake: Both the good and evil Willows' faces are barely seen onscreen at the same time due to them being played by the same actress, but when they occasionally are the good Willow stands out from the picture more than the evil Willow. She must have been filmed separately from the good Willow and edited in later.