The agent was correct. If you are using miles from an EXP account, but an EXP member is not traveling on the same PNR, then the phone/airport ticketing fees apply. It has always been that way, at least since I became EXP. I often use my miles for family members, and I'm always charged the ticketing fee if I'm not traveling with them.
However, the expedite and redeposit fees would NOT apply, since the miles came from an EXP account.