The wearing of poppies by fans is among the incidents being investigated by FIFA, according to the Football Association of Wales (FAW).
World football's governing body opened disciplinary proceedings against the associations of Wales and Northern Ireland on Wednesday after both countries marked Remembrance weekend at World Cup qualifiers.
While refraining from the wearing of poppies by players, which landed England and Scotland in hot water, the poppy symbol was displayed in mosaic form ahead of kick-off and black armbands were worn.
The mosaic is one of the incidents being looked into by FIFA, along with a banner depicting the poppy displayed by supporters and a bunch of poppies carried by a member of the armed forces.
But the FAW also says supporters wearing poppies in the stands form part of the investigation.
FAW chief executive Jonathan Ford said: "Naturally as an association we are disappointed and surprised at the news. Our intention was to show respect on Armistice weekend which we feel we did in the right and proper way.
"We also adhered to the rules and regulations of the competition and the communication from FIFA prohibiting the FAW request for the players to wear the poppy symbol on the armbands or the field of play.
"We are particularly disappointed that one of the charges relates to supporters in the stands wearing poppies. Naturally as an association we will strongly contest the charges."
The case will be submitted to the FIFA Disciplinary Committee for evaluation on December 9. The FAW has until November 29 to provide a statement and relevant evidence.
The Irish FA has vowed to "robustly defend" the charges levelled against it.