Masquerade - S2-E7
Plot hole: Why did Stefan and Damon suddenly decide to abandon their plans to kill Katherine when the spell linking her to Elena were broken? When only moments earlier, Damon said "The second the spell is lifted, I'm gonna drive a stake right through your heart." So that begs the question why did he never follow through? Why instead place her in the spelled tomb that you know can be dispelled? It makes absolutely no sense when you think about it.
Answer: Because Lily's humanity was not turned off as Elena and Stefan's were...therefore she had some control over her actions and had a conscience whereas the other two did not at the time.