Example: Javelin has 38 rounds total (8 in the mag, 30 in the ammo pool). If I'm empty on ammo and use the refill station I get 30 rounds for the ammo pool but the current magazine remains empty. So to fully restock I need to pay twice and do an extra reload animation.
The intent of the ammo refill station appears to be fully restocking ammo. If using the station on empty it should trigger a reload animation and provide the full 38 rounds.