I've run into this for the third time what happend is that I deafeated the phosbat boss on day 7 but couldn't bring the fruit back in time so on day 29 I came back to collect all the fruit before the end of the game and used flying pikmin to pick up the fruit and they got stuck also they still count as if their with us even when I was far away on the map. They also they ignore the whistle