Is there an expiation for violating the deceased's dying wish to have his country's flag placed on him, a wish that was not remembered or carried out at the time of his death?

There is no blame upon you for not executing the will, and this does not necessitate expiation or any action. What will benefit your father is righteous deeds from your supplication for him, your seeking forgiveness for him, giving charity on his behalf, and performing Hajj and Umrah.