Egentligen ja. SHIELD infiltrerades av Hydra i serierna.
After the events of Secret Invasion, Nick Fury discovers that S.H.I.E.L.D. was under the control of HYDRA, and apparently had been from the beginning. He also discovers a number of organizations under HYDRA's alleged control including the United States' FBI Science and Technology Branch, NSA and US Department of Treasury, as well as the Russian Main Intelligence Directorate and Foreign Intelligence Service and the Canadian Security Intelligence Service.
-Secret Warriors #1