Infield fly?
I hadn't thought of that, but I don't see what that would have to do with it. There should have been no force play at second base (because the batter was out), and yet there was.
Also the official score does not mention the infield fly rule, nor did any of the commentators.
The Infield Fly Rule only applies with runners on 1st and 2nd or bases loaded with less than 2 outs. In that case a fly ball that can be caught by an infielder with normal effort results in the batter-runner being declared out and the runners may advance at their own risk. The scenario the OP described was not an infield fly rule situation. With a runner on first and a line drive caught by an infielder the runner on first does not have to advance and certainly would not be declared out by the infielder stepping on second base. If that call was made they would still be arguing. The OP must have missed something. There is no way the call would have been made the way it was described.
The runner at first had taken a lead off the bag. The liner to Short would have required the runner to tag-up to advance. Since the Short stop tagged the advance bag before the runner got back to first to tag up the base runner is out.