Thank you for reaching out with this beekeeping question!

In case you didn't know, some beekeepers do store wet supers after extracting honey. Combs that have only been used to store nectar and honey are usually less susceptible to pests, whereas combs that have pollen or that were used for brood rearing may be more susceptible to damage from wax moths, etc. To store wet supers just used for nectar/honey, I usually stack the supers on a solid base (or on a bottom board with something to close the entrance) and a telescoping cover (or something similar). I usually stack the equipment in an area that gets cold over the winter, like a barn or under a lean-to. For colonies that may be more susceptible to wax moth, you can use a product labeled for use in honey supers, like Certan or Para-Moth.

When I want the bees to clean up honey from extracted supers, I put the supers in between the inner cover and outer/telescoping cover. Since there is a divider (inner cover) between the broodnest and the supers, bees will often (but not always, in my experience) move honey from the extracted supers to the broodnest.

Some beekeepers set up a "robbing station" of extracted supers they want bees to dry/clean up. They set extracted supers outside in a space that is far from human, pet, and livestock activity. It is best if the robbing station is also far from the apiary. In addition to a frenzy of thousands of honey bees (and other insects like wasps), robbing stations may lead to disease transmission between honey bees. For this reason, I don't usually recommend or use robbing stations, but it is a fairly common practice.

To answer your specific questions:

Did I leave the extracted equipment on too long? It's very hard to predict late-season nectar flows, and they can vary quite a bit from year to year and location to location. Healthy honey bee colonies will continue to collect nectar as long as it's available in the environment and weather allows for foraging.

Is there harm having uncapped frames in the hive going into winter? It may be fine, but we usually prefer that the top box is full of dried honey/syrup. Honey bees usually cluster low in the hive and move up throughout the winter as they consume food stores. 

What do I do with the wet frames that didn’t go back into the hives? You can stack and store the wet supers or try to put them between an inner and outer cover (especially while we still have warm daytime temperatures), as described above.

Happy beekeeping!