You may have also lost a general which will actually decrease your military score until he's replaced.
It's also possible that you have LESS soldier POPs than you did before the war. Military score is calculated from your potential number of brigades, not how many you actually have (though this indirectly attributes to score during wartime since the more brigades you have, the more supplies you need). If you had 80/100 brigades during your war and now have 90/95, your military score will be less even though you have more brigades than before.
These are the most common causes of lowering military scores, at least.