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It's been almost a week and still no solutions. I think we may have to just put up with this bug and hopefully it doesn't appear too often in the future.
How did it happen? Can you give the circumstances? There are a few conditions that automatically end a combat, but they are uncommon. Typically it is something stupid, such as Autonom Network Controllers just leaving combat for no reason, or some such.
 
I've suspected that it is likely to do with either a particular unit/mod, or a certain effect. But without a good log output, it is hard to determine exactly what the issue is.