The agent screwed up.

The pilots screwed up.

The IT is screwed up.

For me this is a revealing part of the article:

"United sent pilots a weight estimate that assumed the coach section of the Boeing Co. (BA) 737-900 was empty when it was full, according to three people familiar with the incident who asked not to be named because they weren’t authorized to speak about it."

When employees in a company go to the press in covert whistleblowing it reflects how bad morale is and a complete loss of faith in their management to be able to fix anything.