I encountered this problem now, I did found her very early (not sure, what time, I think it's before the first DLC come out), but I didn't recruited her after goes outside and used up her dialogues.
And then I start the DN079 quest "Mystery Meat", completed it by "Alternative shortcut" way and then killed Theodore Collins.
Check the wiki for detail of the "Alternative shortcut".
http://fallout.wikia.com/wiki/Mystery_Meat
And after a years later, now I decided want to recruite Rylee but whatever I do, she just has no option for recruite at all, as the quest's bug section of the wiki wrote...:
(PS4 & PC) As of patch 1.08 on the PS4 & PC, it is possible that she will not offer in dialogue the option to be recruited if one has already completed "Mystery Meat" and meets her later. The dialogue option of "People getting sick?" may remain even after it has been discussed.
However, it is possible to use console to move her to settlement and make her your lvl 4 merchant, but the "People getting sick?" will remain. (If you use console to teleport to her, you find yourself in the sandbox)
http://fallout.wikia.com/wiki/Rylee#Bugs
So she just bugged, even prid 3eff3 then moveto player and do some console command tricks to make her my settler but just doesn't works.
(sqs DN079 command shows that quest still running and on stage 951, but the quest in my pip-boy was moved to completed quest section, I don't know if related or not...since I were not "proper" complete the quest by using the "Alternative shortcut" method I guess...)