A first-half goal by Nelson Valdez was ruled out for offside and then when Oscar Cardozo had a penalty saved, Spanish players were encroaching but no re-take was ordered - though the referee did order a re-take for Xabi Alonso's penalty minutes later.
Referring to FIFA president Sepp Blatter's apology to England and Mexico over refereeing errors last week, Martino said: "No doubt FIFA will apologise to us - so say thank you to FIFA for apologising to us.
"The dressing room is as it should be after a tremendous effort, we have played with all our heart and lost the match at the very end. We played with Spain on an equal footing but we were not lucky, it was not our night.
"I feel very proud and I have congratulated my men in the dressing room and I know everyone in the country feels very proud of the team who has represented them.
"I don't feel happy or satisfied - we were trying to make history. Spain are in the semi-finals but we could have been there too.''