Thread:Shabook/@comment-1509585-20141101144503/@comment-112155-20141101144948

The source is from CATWS, they are "affiliated" willingly or not, maybe as test subjects, maybe as prisoners, or maybe as willing members, but they are shown to be "affiliated" to them. That doesn't mean they are members of HYDRA (and hence probably your confussion about it).

Simply put, affiliations are not always "positive".

Of course, that affiliation, whatever it is, is going to change once Age of Ultron premieres and the become Avengers