I think that is still broken. Pretty sure it counts the units a player suicided as killed. Same with buildings, if you delete or even just cancel one of your own it counts it as razed. Taking out and putting relics into monastery re-counts them as collected.
I made a thread on this in Discussion too, Why is the score screen so miscalculated? - #10 by CRothlisberger
I think military score is related to time in combat. I had a game with a really high military score yesterday, even tho my army of gunners was just sitting afk shooting down a landmark for 15 minutes while my allies did all the combat.