<p>Hydra was hiden within Shield. They became actual agents. Getting uniforms wouldnt be that hard.  </p>

<p>@Wikia contributor - that would mean Loki could have known who within S.H.I.E.L.D. was HYDRA.   That way he had willing minions.  Look at the attack on the hellecarrier - it was a show of force.  Loki would not have been able to mass hypnotize a group of people; he would have been able to pull that off in Germany.  He only used the mind control scepter on a select few (Hawkeye, Selvig) because they had key skills and information he wanted to aid in his invasion.   Since the scepter was left behind and ended up in HYDRA's hands, probably experimented on it to come up with the idea of Whitehall's mind control device in Agents of S.H.I.E.L.D.  I would not be surpried it comes out in Age of Ultron that HYDRA formed an alliance with Loki for its own purposes. </p>