My bees haven't filled up the super yet, and it's starting to get colder and the bees aren't working as hard during the day. The super has some capped honey, .....What temperature does honey crystalize at?
You can let the bees rob honey to hive or just put the box in the store. If it is moist, and about +10C, honey starts to ferment.
Like golfpsycho says, do not take it as a problem.
But if you exract honey from combs, 20% of honey yield will stay in comb walls. There is no difference with that case.