Defender James Collins's dismissal after just 25 minutes proved to be crucial in this Group A fixture, as the Dragons went down at the Millennium Stadium in Cardiff on Friday.
"For me it's not a sending-off," Coleman told Sky Sports News. "And there were one or two challenges on our boys as well that went unnoticed.
"The free kick they scored from at the end wasn't a free kick either, so maybe the referee just had one of those nights.
"He certainly could have been kinder to us in certain situations but they're a good team and fair play they got the result."
Wales are away at Serbia in their second qualifying game on Tuesday.