I have seen this go haywire a couple of times in Seattle. The TSA agent was not able to scan the phone, so he sent them back out....after they had waited in line, they had to do it all over again. One guy was a complete jerk about it, knocking over the ropes as he went under them.
I personally will always print my boarding pass for that reason alone. I never want to be sent away, only to return and have to stand in line again.