I think its a common problem in the game - I reckon each of my settlements is missing between two and eight people.
My worst case is Sunshine Tidings Co-op. There are supposed to be fourteen people there, but I can only find four. I do know that I assigned three as provisioners (before I knew that you only need one link per settlement), and one was killed in a raid, but that still leaves six missing. Actually, I think there are eight missing, because another two sent from other settlements never arrived.
Its very frustrating; the settlement simply won't develop much, as there are not enough people to do some farming and man the shop/bar/clinic in order to get happiness or whatever up.
I also don't know why recruitment just stops at some arbitrary point. My settlements have lavish facilities and my base Charisma is 10, but not a single place has edged past 22 - anything over 18 I reassign to the ones that can't seem to recruit over about 12 total. Abernathy Farm has never recruited past 8 itself, despite having a vast surplus of food, water and defence available (and my own personal protection in the form of those endless Minutemen quests!).
(I don't run any mods)