I was playing a Manhunter deck and was playing against someone playing the same.He made the comment that you couldn't play multiple copies of sleeper cell because they aren't army.Since they aren't recruited,doesn't that negate uniqueness?

it doesn't negate uniqueness, but you only check for uniqueness when you recrute. since the sleeper agents are "put into play" and not recruted you can have multiple copies of them in play as long as you don't recrute them.