This is weird, but are little sisters supposed to respawn? I'm up to Neptunes Bounty and I've gotten the first 2 little sisters but after getting the second one I look down to the lower wharf and see there is another one. Try to get it die and then go back up and the little sister from the upper wharf is there again! I could get both plus the other sister later on and get 5 little sisters. How would it effect the game and does anyone know how or why this happened? I'm scared to get any extras, haha.

Some levels seem to be bugged, there are known extras in certain areas. I'm not sure if they count towards the endings though, so if you're going for a particular ending you might want to rescue or harvest consistently (or just check the wikia.)

It doesn't matter which ones you rescue to complete the level's quota though, they all count.