I think its the pokemon's level. I have a level 10 dragonite which is last with a higher
level poke in front of it. (25-30)
If you want it like before remove them all from the team except one and train.
Btw:leader will always be front.

Do u mean in a dungeon? Well if it is it goes like:

1st: leading , the main charecter or pokemon made leader! (leading pokemon)

2nd: your partner pokemon or a pokemon chosen to fill the role

3rd: your third choice pokemon, one of the extra partners

4th: just like before but your 2nd extra partner!

Btw: after beaten game you can change leader and take off partner pokemon and replace them
temporarely!!

I hope this helps and makes sense!!!