I find it extremely hard to believe that an "enemy" aircraft could fly over the base undetected. We knew when mortars were coming in, surely they knew of aircraft flying overhead... The aircraft was super quiet and we couldn't hear it at all. In any case, I know people think I am crazy when I talk about this so I guess I would just prefer to leave it alone now and wish I hadn't brought it up.
Please don't get me wrong: I'm certainly not thinking you are crazy. My bet is that your government is quite certainly capable of trying out stuff on their own soldiers. And I suppose also that it's not the Afghans who possess this kind of quiet undetectable technology. So who else in or around Afghanistan might possess it? Apart from the American army, I mean. Inside the country you would have allied forces like the French or Germans who might possess quiet aircraft - actually I've no idea, but if they they did, it would however be difficult to find a motive for them to secretly spray stuff on their american friends.
So lets look outside the Afghan borders. Who could be lurking there, not an official enemy at the moment, but not really american-friendly either and who could be in possession of highest advanced technology or being allied with a country who does?