I doubt theft was an issue here. These cards can only be used by the person who owns it. Also, the fact that the card was on top of other stuff makes it highly likely it simply slid off while going through the xray machine.

Still, the agents should have taken the time to resolve the matter - but having such a lightweight card on top of other stuff is asking for it to be 'wiped off' by the plastic/rubber strands in front of the xray machine.