Michael Higdon scored the first of his brace at Tannadice with just two minutes on the clock and Henrik Ojamaa doubled the advantage six minutes later.
McNamara was disappointed in the way his charges conceded the goals, but he praised United for coming back into the match.
Motherwell keeper Darren Randolph made several vital saves throughout the match restricting the hosts to a solitary Jon Daly goal.
McNamara said: "The first one was a good strike and you can't take anything away from that but we maybe could have stopped the shot.
"The second one was disappointing, from a throw-in, and he ran right through. It wasn't good defending.
"We battled hard and had a few chances where their keeper has done well.
"I knew the next goal would be crucial and I'm disappointed it wasn't us that got it."