I had a similar play last night in a HS spring league. A1 has a FC endline throw-in deflected into the BC by A3 then A3 runs to pick up the ball... I had nothing, well except a new 10 second count (much to the surprise of my 2 veteran partners). At the next TO my reply was simply "although the throw-in ended on the deflection, there is no team control on a throw-in, TC began when A3 possessed the ball".

I believe the same holds true in your sitch.

Not sure about NCAA...