Effective your online booking failed and you ended up doing a phone booking requiring a phone agent due to your error. So the phone fee is not surprising.

You might get a "one time adjustment" or cert if you call back. Not sure what UA did wrong other then following the rules literally. A proactive compassionate move by the agent was a missed customer service opportunity.

An alternative would have been to cancel the original reservation or let it expire. Then do a new booking online and avoid the phone agent fee.