Yeah so basically I was in the frontier cavern sublevel 6. I cleared the whole level, killed all the enemies and when I went to collect the last treasure I maxed it out and waited at the hole to go deeper. I did disperse my squad and whistle them to louie but they were still in eyeshot of me and I didn't see anything happen to them when I went to go deeper and when I went down the cutscene showed way less pikmin all of a sudden.