At first, excuse me for my horrible English. I don't speak the language fluently.
After the First Curse is undone by Regina, everyone is sent to the Enchanted Forest, except Henry, for being born in the World Without Magic, and Emma, for being the savior. In the case of the Lost Boys, some of them later were seen in Storybrook and others in Neverland, but ... why?
They were not affected by the First Curse and probably not all of them came from the Enchanted Forest (after all, the Shadow of Peter Pan can travel between any worlds). If they returned to the world they were before they went to Storybrook, everyone would go to Neverland, which would explain why some were there later, but how could Snow White's curse affect them if it did not affect Pan when Regina launched First Curse?
In case they returned to their original worlds, it would even make sense for some to return to the Enchanted Forest, but why were some of them still in Neverland? Were children born there? If they were born, whose children would they be? From Tinker Bell? From Hook? From Pan? In the same way, we might also assume that some of them who were born in the World Without Magic simply stayed where Storybrooke should be. Lonely children in the middle of the forest.
As seen in S3E9 "Save Henry", Emma offers to take the Lost Boys back to Storybrooke with her and several of them choose to come with her and the others on Hook's ship. When Regina's curse is undone, everyone is sent back to where they came from and as seen in S3E4 "Nasty Habits", several of the Lost Boys come from the Enchanted Forest. Therefore, the ones who came from the Enchanted Forest are returned to their original home world when the curse is undone and are brought back to Storybrooke when Snow White casts the second curse.
As for why some of them were still in Neverland, it's most likely because not all of the Lost Boys chose to leave with Emma. Seems like some of them preferred to stay.
If I remember correctly, not all the lost boys left Neverland as we saw in season 6. Those that rejected Malcolm left Neverland and the last time we saw them was that they were at Baelfire's funeral too. At least that's what I remember.