As Sotek said, the corrupted aether isn't caused by allagan technology or any other technology for that matter, at least not directly. As far as I remember from 1.0, Dalamud was sucking aether from Eorzea and when it finally released Bahamut, it was scattered throughout the land. All those chucks of corrupted aether are parts of Dalamud. I imagine that some of it also fell off of Bahamut as he was wreaking havoc on Eorzea.