Shelby:
I had the same thing happen when tried to make a flight reservation-We must be in the group of lucky ones. The UA website also charged for Economy Plus seats-I have an E+ subscription.
When I called the Reservation Line to book the same flights, the agent was able to book E+ seats without any additional charge and was willing to waive the fee for making the reservation.
My hope is that the website has a temporary glitch that will quickly resolve the issue. If not, I hope that other Reservation Agents will be willing to waive the booking fee when I call to make a reservation.