Well thats what I think about the flashbacks, but wouldnt it be more suitable that he would get flashbacks about actually assassinating the people he was sent out to assassinate? To me that would have made more sense for that explanation, or Spielberg wanted to blame the munich attacks for this guys problems (feeling guilty about what he did) as if, if it wasnt for those attacks, he wouldnt feel any of the guilt and/or fear he is feeling at the end.

I think the flashbacks at the end of the movie were due to the inner impact of the crimes he did during the past years of his work for the Mosad .. if you recall his conversation with his direct boss before the end and the questions he asked him .. it seems like he started realizing that killing the enemy is not the answer to the problems!.

Losing his people got to Avner, and thats why he was loosing it. And adding to it was his curiousity, he wanted to see proof for killing these people which he wasnt given. So it slowly got to him, everything added up.