When Cole complained to the male employee, she claimed he patronised her by referring to her as "honey".
"The first person to check my ticket was very abrasive. His response to my explaining the situation, politely and honestly, and that I wanted to complain, was 'you go ahead honey'. In the context and given his aggressive tone I can only assume he didn't like being challenged by a woman," she told the BBC.
"I wouldn't have complained if he'd used the term in a familial or affectionate way. It definitely wasn't that."
However, the original gaffe snowballed after Ms Cole sent a public tweet regarding the incident to the Virgin Trains East Coast Twitter account.
The original tweet read: "When virgin trains mess up and the older male train manager in the resulting conversation dismisses you with that hideously patronising word women shudder at in contexts such as these: 'honey.'"
Cole said she was "stunned" by the company's response, after they posted: "Sorry for the mess up Emily, would you prefer 'pet' or 'love' next time?"
The company was immediately inundated with accusations of sexism, and the tweet has been deleted.
While some Twitter users accused Cole of overreacting, many offered their support.
To their credit, Virgin Trains apologised "unreservedly" for the tweet and for the "offence caused".
But Cole was not impressed, tweeting: "Wonderful to see that @Virgin_TrainsEC take complaints of rude and misogynistic behaviour seriously. Stunned."
Some Twitter users have questioned what the repercussions will be for the staff member who sent the tweet, but the company is yet to respond.
But the latest furore is just one of many controversies which have plagued Virgin Trains.
Just last month, UK millionaire businessman James Timpson called the rail operator a "disgrace" after his 15-year-old daughter was abandoned at a London station alone at night.
Yesterday there was chaos on a Virgin Train when a customer left behind a pet scorpion, and in 2014 a Virgin Trains passenger was slapped with a whopping $1,900 fine for simply purchasing the wrong ticket.