Plot hole: When Andrew wakes up, Anya mentions the First posing as Warren to make him kill Jonathan. Jonathan's body hasn't been found and the only time Andrew became ready to talk, he was knocked unconscious. They shouldn't have a clue about Jonathan's murder.
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)
Get It Done - S7-E15
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: 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.
School Hard - S2-E3
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 Ampata is first released from her imprisonment, why didn't she break the seal then? She knew the only way to re-mummify her was to put the seal back together, so why not shatter it completely instead of leaving it in large fragments? (00:08:40)
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: How did Buffy know where to find Riley at the end of 'Into The Woods'? He told her he was leaving with the army, but he never mentioned the helicopter pad. (00:40:30)
School Hard - S2-E3
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: In "I Robot, You Jane", how exactly does Willow scan Moloch out of his book when the scan is only about two thirds the width of it? (00:04:25)
Chosen answer: From what we see in the series, certain girls are identifiable as potential Slayers - Kendra clearly fell into this category. The identification method is presumably mystical in nature, but the Watchers' Council are pretty effective at that sort of thing, so they're quite good at tracking down the potentials ahead of time. Not perfect, though - it does appear that Buffy herself may have slipped through the net - certainly she had no inkling of what she was until she'd already taken on the role of Slayer. It is possible, however, that this was actually cultural - an American family would hardly be likely to turn over their daughter to some strange man for 'training', so the Watchers might have chosen to keep an eye on her covertly, whereas some other cultures (like Kendra's Jamaican parents) might be more willing to believe.
Tailkinker ★