Continuity mistake: In 'The Initiative', Riley, Graham and Forrest are looking in through the windows of Stevenson Hall with thermal goggles looking for Spike, they see him walking towards Willow. When we see Willow and Spike seconds later he is still sitting on the bed where he was for most of the scene. (00:37:30)
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.
Visible crew/equipment: In the scene where Spike escapes from The Initiative a black curtain can be seen to the right of the screen after the other vampire is release from his cell. The curtain serves no purpose to the set or scene and it disappears in the next shot. (00:13:25)