Further testing, the issue we have relates to grouped layers in the table of contents of the Web App. Previously we had for example, several districts that were all checked on, contained in a group layer that was checked off by default. So if a user wants to see all the districts, they just had to check on the group. After the November update, when the app "auto-saves" on close, the next time you open the app, the grouped layer and all its subordinates are all un-checked. So the user who was used to just checking on the group layer, now does so and nothing happens. They have to expand the group and check all the layers on one by one.
I checked the ArcGIS.com map that controls the Web App, and group layer is un-checked and the subordinates are still all checked as they should be, and as by design before the November update.