Sounds like you need a recruit cage, which can be purchased from the gate menu before you head out! Make sure you have 1 empty cage per character you hope to fill. Upon re-entry to the city, the cage is cut apart and disposed of.
The other problem may be that there's someone else left alive! Your recruit must be the only living enemy left!
(Side note: You can also use a Spidaur to snare and recruit the last remaining enemy fighter, as long as you have a recruit cage with you!)