Captain Ramsey and winger Bale, who scored the opener in today's victory, have courted controversy by appearing in promotional images for a Team GB supporter shirt.
The FAW do not wish their players to be involved in Stuart Pearce's squad for the London Olympics as they fear it will have a detrimental effect on their status as an independent footballing nation.
The players' names were applauded when they were read out ahead of kick-off, although a 'No Team GB' banner was briefly unfurled at one end of the ground.
However, a group of fans made their feelings known to the pair as they boarded the team bus outside the stadium following the game.
An FAW spokesman said: "There were some fans who chose to voice their opinion over the issue of Team GB selection, but we had security people with the team so the players were never in any danger.
"We respect the right of our supporters to an opinion."
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