The Latics opened the scoring in the 19th minute when Jean Beausejour's corner was only cleared to James McCarthy on the edge of the box and he drilled his shot into the bottom corner via a deflection off Jamie Mackie.
The visitors hit back, though, with Wigan failing to deal with a set-piece allowing QPR captain Ryan Nelsen to head in his first goal for the club from Adel Taarabt's corner.
Rangers took the lead with 19 minutes to go through substitute Djibril Cisse only for McCarthy - who had not scored for almost two years prior to the game - to poke home his second three minutes later.
It was the Latics' first point in three games but Martinez felt they deserved more.
He said: "We are disappointed because to concede two goals is always frustrating. I just feel that for us to score a goal we need to be perfect.
"The first time that QPR get in our box they get a free header and then in the second half they didn't have an attacking threat but they got in front.
"But I was very pleased with the manner in which we reacted to going 2-1 down.
"It would have been all too easy to panic, to lose our composure, but I thought we were very mature and we're disappointed we couldn't get any more because the chances were there.
"I thought Robert Green had an outstanding performance and in many ways I thought we deserved the three points."