Sounds like they should have called it. But having not called it, you can't go back and "fix it" after the fact. It's a judgment call that has to be made on the spot or not at all.
The whole point of making the call while the ball is in the air is to alert the runners that they can hold without fear of being put out on force plays. The infield fly rule is, after all, a rule designed to prevent what were considered unfair double plays.
So once the ball has hit the ground and everyone is safe, it can't be called then. It certainly cannot be called to benefit the defensive team. The rule exists to help the OFFENSIVE team, though this is something commonly not appreciated since an out is involved. For the defensive team's coach to go out there and argue that he should get an out on the play is kind of silly. All his team had to do to get the out was to catch a pop up. He can't blame the umps for the muff.