However, the situation was soon defused and the two parties went their separate ways.
Reflecting on the incident, Bowen has insisted that the confrontation helped produce recent positive results against Liverpool and Arsenal.
"Squad and management got on the coach from the station to go back to the training ground and the first thing I said to Mark was 'That's fantastic'," Bowen told the London Evening Standard. "He gave me a strange look as though to say 'What's fantastic about getting abuse thrown in my face?'
"I said 'We've won one of the last 10 Premier League games and have got to the stage where out of 100 fans, I think two were a bit out of order. The other 98 were prepared to listen and help put right the couple who were over the top. I don't think too many clubs in the country after the last 10 games would have so few complaining heatedly.
"Since then, of course, we've gone on to beat Liverpool and Arsenal and the fans have given their team brilliant backing. And I remember the first thing Mark said back in his office after that was 'Jeez, if we can get this going, give these fans a bit of success over the next few years, we'll have some fun here. It's a great place, they're crying out for it'."
QPR face Swansea City at Loftus Road this evening.