If they are not travelling with a gold, then they are not supposed to be in the elite seats. If you however book from your online account, the system sees your gold status and allows it.. What likely happened is an aircraft swap/sched change at some point which caused him to be put in another seat. If you want to PM the record locator I can look.

Agents are not going through to throw people out of seats. But if they did need to re-seat anyway due to a sched change, then they are not going to reseat him into an elite seat.