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?
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: 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.
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 the flashback to Buffy in L.A., how did Angel get there with the front windshield of his car blacked out? Being a vampire, he obviously needs it during the day, but he also wouldn't be able to see traffic. And it just seems to be too much of hassle for him to remove it at sunset, just to reapply it at sunrise, just to remove it again, etc.
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Plot hole: After losing his soul, Angelus kills Jenny Calender's uncle, who is a descendant of the gypsy clan who cursed him. But, since there is nothing to suggest the uncle's room is in a public location, Angelus couldn't have gotten in the room without an invitation.
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Plot hole: In 'Becoming, part 2' Spike decides he doesn't want to see the world end and makes an alliance with Buffy. Later on, however, he helps Angel get the information he need from Giles to end the world. If he's trying to save the world, why help Angel destroy it even faster? He didn't need to buy Giles any time - he had already convinced Angelus to keep Giles alive for the time being. If he had truly reached breaking point later on Spike could have called in Drusilla then, but as it is he helped Angelus way too early and nearly cost Buffy her life. [Some people disagree at great length, others don't - I haven't seen the episode myself, and the explanation of the mistake and the corrections just make my brain melt. File this under "make up your own mind and just let it go"].