This one is a legacy from previous Arma series.If you have two playable AI squads and an empty vehicle\chopper, when you switch to the second squad the previous squad will disembark automatically.
Basically like in the repro mission and vid I uploaded you can't have an infantry squad board a chopper and then switch to a different team(pilots in this case) to transport the infantry team somewhere else because the previous squad will disembark when they aren't under your control.The way they behave now it's quite useless to have multiple playable squads for different tasks.
http://www.fileconvoy.com/dfl.php?id=g17e34a79eaccc901999963232f807e4b13b4fe7e6 (repro mission)
https://www.youtube.com/watch?v=9sDPhNFVuvY