Had a similar event last June: SJC->SNA RT. Bought it on ual.com at $115 but when I went into the ual.com itinerary a day later, noticed that the ticket was not yet issued (paper tix was required a/c of 2 bus segments) and fare was up to $151. Web support was able to see the PNR history. All they were able to conclude was that someone at United "re-fared" the itinerary. Since it hadn't ticketed the web support person chose to protect my lower fare by queuing it to their own in-house agent (get.there.com???) and took over the res. A week later, I got my $115 ticket from a North Dakota postmark agency.
That taught me to check itineraries I ticketed to make sure they weren't re-fared before ticketing. This problem hasn't happened since.