It depends on the story.
If the story was written in a way that perhaps you faced a certain character earlier in the game, and you didn’t know they would end up being your final big bad, but circumstances and story events changed them into something else, then I don’t have a problem with it.
Or you ran into them and the game decided not to tell you yet that they were the ultimate evil of the game. Perfect example is Kefka. Until the end of the first half of FF6, you would never think that crazy fucking clown was going to steal the show and burn the entire world down, making him your final boss.
So like I said, if a story sets it up right and does it well, then no, I have no problem with it.