At the very beginning of the episode 2 The Harvest Buffy gets away from the vampire because he touches the cross that Angel gave her. As soon as she gets out of the coffin the necklace is gone. It's also gone while she is running through the cemetery.Then in the next scene it's back.

*Correction* Because she wasn't originally wearing it, when Luke was going to bite her, she simply placed the necklace on her neck - you can see that it is not attached or going around her neck. Once he leaves, she grabs it and puts it away again. She clearly does not have time to put it on while she is running away, but likely puts it on once she no longer feels she is in danger. We as an audience assume that she put it on once she was safe because she realized that it would be better to wear it. Much like we assume that the characters sleep, go to the bathroom, eat and get dressed when we don't see them doing these things.