Hi Emma,
This is the reply I left on the United website complaints thread stickied at the top of the United forum. It easily applies to your situation. Try to be calm and patient and do the following:have the suport agent manually enter all of the data needed to do the booking. In my case I could not apply an ECert.
You have to call the United web support desk at 1-800-589-5582 and take the following steps. Tell the agent the exact dates, times, and flight numbers you wish to book. Then tell the person the exact fare code basis which you want reserved. Then explain to them that you are not able book because you keep getting error messages. The web support agent may incorrectly tell you that you are booking a circle itinerary or that your flights do not qualify for the Ecert. Be firm, but assertive. As long as you are booking a round trip, you should be able to get what you need accomplished.
Politely ask the agent to contact the support desk and manually enters the following: the flight numbers, the fare basis code, and the E Certificate number. Before you purchase the ticket, make sure that you review the dates, flights, and the fare code basis for your complete itinerary. Make sure you get the fare basis code that you need, as web support may by default will book you into a very restrictive fare code. Also know what the fare cost before the ECert was applied. This may take some time and be cumbersome, but it can be done! It took me an hour and fifteen minutes to do exactly this yesterday, but I got to see the light at the end of the tunnel.