I am in Michigan, USA and it has been raining for 3 days. I went ou to check the bees and when I looked into the three windows of the Flow super I saw moisture condensing on the inside. It was also really hard to get the lower tray cover out as it has swelled with the moisture. I am concerned as we are getting into winter and I want to avert a moisture problem. Is this normal? If not, what can I do?
Pretty typical to see condensation on the windows, since it is much warmer inside than out.
The wood swelling might be an issue, just make sure there’s no debris on the edges of the cover or the base where it goes. Assuming the wood is well finished, you could fashion a sort of awning to keep water off or and consider sanding it down if it is too tight when damp.
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You probably ought to have the Flow super off the hive by now. If you haven’t already, I would make some plans for insulating the hive and perhaps building a moisture quilt. 
@Tom_Frederick is in southern Michigan - he might be in the middle of his fall aster and goldenrod flow like we are in central OH and like @Eva in eastern PA.
But for sure, the bees luck can change rapidly this time of year, especially if there’s a lot of rain or unusually cold temperatures.
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It is possible to have a second harvest around now, but I aim for finishing that before mid-Sept give or take, and capped or not. (I have yet to find large amounts of unripe honey/nectar even when uncapped - @Dawn_SD pointed out in another post that bees don’t always bother capping when they know they’ll need it soon). Plus, I have a medium box on top - since mid spring - that helps draw air up & away from the Flow frames, which helps dry what’s in there.
My Flows are off after a nice (smaller) second harvest, but there’s still some good forage around. The later the forage, the less appealing I find the resulting honey flavor to be. Also, the later stuff tends to crystallize more readily - another reason I want to leave it for the bees, because it’s so suitable for wintering feed & a bit of moisture control.
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