Plot hole: When Prue first releases Matthew, he blinks several times, then blows out the windows and jumps out. Why would he do this and reveal who and what he is when he could have simply blinked? Obviously it was just a way to get the police involved so Andy could be chasing Prue through the episode.
Plot hole: When Andy, Phoebe and Prue are in the attic figuring out how to vanquish the ghost of Alcatraz, pages starts flipping, the book opens up to the page where the truth spell is, and Andy finds out that Prue cast that spell on him. Later when he asks how much time Prue gave him to react, she says "a minute or two". But in the episode "Truth is out there" (1-8) it was first in Prue's office when she told him, and the clock on the wall shows that it's 25 past 5. And it was 8 o'clock when Prue cast that spell. So few hours later when Andy and Prue are at Andy's door, it's almost 8 o'clock and Prue says she needs the answer now. So doesn't Andy have more like few hours rather than few minutes to react?
Plot hole: Throughout the series, it's established that good witches don't freeze. In this episode, however, Little Piper freezes Future Prue and Piper when they come back to the manor to "kidnap" their younger selves. Simply because the Charmed Ones reason that only one "set" of sisters (past/future) could have their powers doesn't mean that Future Prue, Piper and Phoebe aren't good witches. In other time-travel episodes, the sisters remain immune to freezing and are still able to say spells make potions, meaning they are still good witches. For example, in Season 8 "Forever Charmed," Piper and Leo go back to 1975 (the same time-period as this episode) using Coop's ring, trying to find when Phoebe is alive again. However, when a startled Patty tries to freeze them, only Leo freezes. Piper does not, though she likely cannot use her freezing/exploding power in this time.