In the manual it is stated that "If there are any Action tokens on Favor tiles and Bonus cards remove them from there."
I don't understand how there can still be action tokens on bonus cards if in order to reach this last phase every player has to pass thus returning his previous bonus card and with the newly taken being face down.
As a practical matter many folks (our group included) physically takes the marker off of the bonus tile when they return them to the pool at the time that they pass, but there's nothing saying that they are actually removed at that time even though it'd be impossible for anyone to use them again given the current powers. But technically they aren't really removed until that step. That's all.