not alot of detail in your post, but im pretty sure this is a duplicate combination of these bugs:
This one Kafka decided would only be related to the visual aspect of the battle count (even though points are indeed lost)
This one would be for the points lost in the case where a battle is not being counter and/or any other scenario.
These are very real problems that happen every GWs to roughly half of guilds. they are being tracked and worked on already 
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