Badass Decay: Happens to Malcolm in the third game. He loses all of his magical powers. While he was a psychopath in the first game, he is reduced here to a mischievous guy who wants revenge and wants to clear his name from the death of Brandon's parents. Yeah, as if it were the only bad things he did in the first place...
Many players dislike greatly the Serpent Grotto maze in Fables and Fiends, where you have no clue into which direction to go, have to go through trial and error to find the right way and drop shiny berries on the way because if you get in darkness, you are killed by monsters.
The jungle maze in Malcolm's Revenge is just as hated for pretty much the same reasons. You'd think they'd have learned.
Unwinnable by Insanity: In Fables and Fiends, you can burn Kallak's note in the temple brazier instead of giving it to Brynn. It's difficult to do this unless you deliberately hover over and click on the brazier after clicking on the note, which makes this go beyond Unwinnable by Mistake.
Viewer Gender Confusion: Many players who weren't able to play the games with the voices on couldn't tell for a long time that Brandywine was female.