Since this is TSA were talking about anything is possible (trust me i know this to well especially with meds). Make sure there is a RX label on the epi pen; make sure they dont take the caps off the pen and contaminate it.

Also be prepared to stand your ground on them not messing with or calling it contraband. Its always fun when TSA employees practice medicine without a license. As more then a few have tried to force a "voluntary surrender" of medications for which I suspect were going to be for there own personal use.