Some time ago they did it to me out of KMIA, but I was still able to catch my flight. It's happened rarely as most agents have the common-sense not to be such azzes.
I had the same problem at KFLL trying to jump on AirTran earlier this spring, made me go back to the ticket counter and get a seat req card from the agent,which asked for my carrier's code, then promptly listed me for the flight. Had to voluntairly abandon my liquids at the screening point and run to the gate, but they held the plane for me at the gate, my hat's off to the folks at AT for making up for the jerks at the TSA.