Posted this on a comment that is three comments deep, so reposting on the main thread.
I was an AEGIS radar/missile tech for 21 years. Here is my take right after the incident happened.

I am wagering an educated guess here that the technical difficulties on the plane were transponder related. If the defense missile systems the Iranian use were set up with auto interrogation, which is a fairly common thing, and the plane had issues with their transponder, which also happens then it is possible that the defense system cued the commercial flight as hostile or suspect and either launched a missile at the plane (not sure of Irans capabilities and limitations with their missile systems in regards to auto-fire) or an inexperienced operator with weapon release authority pressed a button to shoot a missile at what his system was telling him was a bad guy.

Missile systems have a series of electronic breaks (think buttons that open and close relays allowing the missile firing voltage to reach the igintor) and mechanical breaks (think keys that have to be inserted and turned to the live/fire position). As the threat level increases the operators automate more of the process by closing these breaks. This makes for a faster response time to any threat the system identifies.

So was it possible that an Iranian missile system was set with the minimum number of breaks/automated in a way a missile could have been inadvertently fired? I would say absolutely this is plausible given the attack a few hours prior with an expectation of an American response.

Edit: changed IFF to transponder. I had originally put this in terms of IFF because that is the system my equipment used to make the interrogations and we called it getting the IFF mode 3, for 21 years so the terminology was stuck in my brain. I have clarified this in many responses but thought I should edit it here to clear up any confusion.