I had fed my pikmin normal nectar earlier in the day. So they still had red and yellow flowers. I fed them the bougainvilleas nectar.
As soon as I hit the whistle to group them together to pick the petals all of my pikmin disappeared. When they reappeared all of my flowers were gone. Every single one was a bud.
Maybe you change squad by double wristling without notice.
Search for bloom in pikmin tab and select the pikmins that appears, click in the nectar from that menu and pick the petals in the next screen.
If someone remains in the search, do it again.
edit: the search have to be done before 4AM because at that time seems that they reset to leaf (you lose the petals)
I didn’t know you could switch squads like that. I found them. Thank you so much!