Tony didn't seem distraught at finding out Clint wasn't still here, but at the same time he wasn't all that pleased wither.

"Uh, know. Only really knew the guy for a day, worked with him to save New York, actually."

If Tony knew Clint better he would have assumed he could have done something to deserve the attack, but as it stands he's just guessing that there could have been more brainwashing happening, or some weird hunger games thing going on at the thyme.