The Armenians complained about some decisions made by the referee and the treatment they had received from the home team, the FA said on its website (www.ffa.am) without giving precise details.
The visitors finished Tuesday's Group B match in Sofia with nine men after Swiss referee Stephan Studer sent off Marcos Pinheiro in the 73rd minute and Gevorg Gazaryan four minutes later.
Bulgaria's Svetoslav Dyakov was also dismissed in the 73rd minute following a brawl involving players from both sides.
