Prestige has nothing to do with Honor.

Honor is a calculation of Net losses during any given PvP battle. It does not factor in who actually wins or loses the battle, merely the resources consumed in the fight. Every military unit and wall defense has its own assigned point value based on its cost to produce.

So, if you won the fight, but lost Honor.... it means that the cost of your losses in terms of production time and resources exceeded those of your opponent.