Recall, Skye was found in Hunan Province in the late 80s (her medical report at St. Agnes was redacted Apr. '89).
Apparently, S.H.I.E.L.D at one time operated a facility named "Shangri-La" in Hunan Province China. Something happened in 1968 that led to this facility being "officially abandoned", but SHIELD's "inner circle" knew that the base was still "active", with China's cooperation, well into the 1980s. It's not entirely clear to me whether the base was still under SHIELD command at this time, or whether SHIELD just knew the facility was still being used, as was the case with the Guest House.
Either way, this heavily implies that either SHIELD, or whoever else may have controlled this facility at the time, played a direct part in creating Skye. It's no mere coincidence that she first shows up right in the vicinity of a secret SHIELD (or former-SHIELD) facility, and then gets fought over by two warring factions. Or that SHIELD just happened to randomly stumble across an "unknown object" in the middle of nowhere (where they happened to also have a base).
I need to go back and rewatch Seeds now, but as I recall, it was a senior agent who called in an 0-8-4. But the backup team who recovered her, were all rookies, and thus wouldn't have known about Shangri-La. Given SHIELD's propensity for procedure, and information compartmentalization, it strikes me as a distinct possibility that the senior agent lied to the rookie team about Skye's origins being unknown, in order to hide the existence of Shangri-La.