Prue claims that in the future she has an "amazing" new office at Bucklands, but it is clearly the same office that she uses in 1999.
When Piper is tracing where the door will go, she draws a line well above her head. When the new door opens it is a different shape and much smaller than she originally traced.
When Prue is looking at the "to create a door" spell, there is nothing between the pages. Seconds later, as she's flipping through the book, she finds the prison map inserted between the pages where the "create a door" spell is, where there was nothing just moments before.
When Leo is confronting Piper and Prue in the town square and they zoom in on the switch hunt poster, a character who is supposed to be frozen clearly blinks.
Future Prue and Piper are flicking through the book of shadows looking for the Return Spell to get back to there current time. They say its not in there, but Prue Actually flicks past the spell clearly written in the book twice in the episode.
It makes absolutely no sense for Leo to think the witch trials will be stopped once Phoebe has been executed, or that indeed witchcraft would somehow stop being a punishable offense that carries the death penalty. Once these things have been established, they are there to stay and it takes decades of campaigning and a societal shift to revert them. Hundreds of millions of people need to change their mind about them, at least in a democracy. But if future America is an autocracy and not a democracy, then all bets are off anyway and the autocrat at the helm of the country would of course benefit from witch burnings to satisfy his followers and consolidate his autocratic powers.