When the game crashes and you restart the game It always remembers all the ammo you have used and removes it but conveniently forgets the experience points you gained.
Since you won’t gain XP during the combat but only after it has ended (either you win or escape the combat) and if game happens to crash during combat, you’ll loose your earned XP as well.
Are you saying the game should remember the combat XP you’ve gained so far, up to the point of game crash? 
Corrected topic title.
//Mod
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I am asking how it remembers the ammo used but not the defeated machines.
Yeah this game has it’s share of memory problems, I haven’t had a bad crash in while, but when I do it’s mostly during a big fire fight and thousands of rounds of precious ammo are gone.
Each time you “Continue” your game, a new machine seed is generated and all machines are respawned (except mission specific machines).
Also, game doesn’t credit you XP during the battle but only after the battle has ended. That leads to a situation where when game crashes during the battle, you won’t get your earned XP credited.