Plot hole: If Spike and his gang only take a few hours to break through the door to Ford's club in 'Lie To Me' (which we are told is six feet of solid steel), why can't Angel break through a thin wire door that visibly shakes every time he hits it, given the same amount of time? (00:38:05)
Plot hole: In 'Graduation Day pt 2' the Mayor has his vampires stand at the bottom of the steps leading out of the school to stop any escaping students. The thing is, all the parents managed to escape out the side exits. Since the Mayor was expecting all the students to try and run too, why didn't he have these exits covered? (00:33:15)
Plot hole: When Dawn and Buffy discover Chloe hanging in the bathroom, Dawn gives a little gasp but nothing more. But, seconds later, some Potentials run from across the hall saying "What is it? We heard -" before they see Chloe. While it suits the next scene to have them there, there wouldn't have been any sounds loud enough for them to have heard from across the hall through a closed door.
Plot hole: Willow and Cordy disappear during a vampire attack. We later see that they spent the entire night hiding out in a closet, but wouldn't Buffy have gone looking for them once the vampires were gone? She knew they had run off somewhere (she mentions it to Giles when she gets a stake from the library). Instead she just goes home, leaving them still missing as far as anyone knows. (00:41:25)
Plot hole: Giles tells Willow to leave him while he extracts information from Ethan on how to break the costume spell. By the time Giles smashes the statue Willow has already found the others, who had left the house where she thought they were and are hiding in a completely different area of the town. No matter how long it took Giles to beat the information out of Ethan, there is no way Willow could have gotten back to the house, realised they were gone and tracked them down before the spell was broken. As a ghost, it is possible she could have happened across them even though they were hiding, but seems unlikely.
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.
Plot hole: When Buffy and Sheila are walking out of school after the meeting with Snyder, Xander runs up to talk to them. He mentions during this scene how Buffy will be helping out at the Parent-Teacher Night, but he shouldn't know this - Buffy only just found out about it in the meeting with Snyder.
Plot hole: When Buffy enters the house to rescue her mother she uses a stake to stop the front door from closing. A vampire then grabs it and the door closes. Why did Buffy use a stake knowing that there was a vampire there when she was almost killed by a vampire with her own stake earlier in the episode because Giles had been injecting her with a muscle relaxant?
Plot hole: Spike must have had his chip implanted while he was unconcious. If so, how did he attack The Initiative scientists without any pain when he tried to escape? You could argue that they programmed him to be capable of violence within The Initiative only, but why would super smart scientists program an evil being to be able to escape at the first opportunity? Joss Whedon has acknowledged this as an oversight.