Plot hole: In the final episode Piper cast the spell with her mother Patty and grandmother Penny to get the Hollow out of (past) Piper, Phoebe, Paige, Billy and Christy. It worked. But in episode 4x13 Charmed and Dangerous, the only way to contain the Hollow is by good and evil working together... which wasn't the case in the final episode.
Plot hole: When Piper goes back in time to save her sisters from dying and get rid of the Hollow, right after Leo describes it as "time catching up with itself" and the new reality Piper takes over her body. Yet in Season 5 Episode 7 "A Witch in Time", Piper goes back to keep Phoebe from saving her boyfriend but once Piper changes the past, the original Piper fades away and the new reality Piper stays.