Jamie Mackie gave the visitors a brief 52nd-minute lead before United scored from successive set-pieces, with Jonny Evans and Darren Fletcher heading past Julio Cesar.
Sir Alex Ferguson’s side wrapped up three points when substitute Javier Hernández added a third, but Bowen is confident QPR have the quality to avoid relegation.
“I would tell the fans: ‘Don’t lose faith’. The quality is there but everything is conspiring against us at the moment. It’s individual errors which are costing us rather than team errors,” Bowen told BBC Sport.
Bowen, who acted as assistant to Hughes at QPR, also admitted his future at the Hoops is uncertain, revealing he has spoken to the club’s sacked manager.
“I really don’t know about my future. It is a good club and a good club to work for,” said Bowen.
“At the moment no-one has said anything to me, but I’m still employed by the club. I played under Harry earlier in my younger days, but he will have his own ideas.”
And on QPR’s former manager, Bowen added: “I’ve spoken to him and he’s obviously very disappointed. But that’s football and he knows it is a results-driven business.”