The vector topographic basemap is the default for our organization but Web App Builder (WAB) seems to be adding another topographic basemap to the gallery using the thumbnail for the application. The basemap widget in WAB is set to use organization default and was not customized. Why is an additional basemap being added to the basemap selector (see attached)? The questionable basemap is not shared as a basemap anywhere in our organization.
Is it possible that there are duplicate layers within the basemap of the web map? This can cause an extra, identical basemap that uses the thumbnail of the project to appear in the basemap gallery.
Try selecting the Topographic basemap from the Basemap tab of the web map to restore its default settings and see if that removes the extra basemap you are seeing in your Web AppBuilder application.
Though I didn't have duplicate layers in my basemap, the reselection of the topo basemap solved the problem. There are a couple of other apps we have that showed this behavior but they didn't have duplicate layers either. Hopefully, these changes will stick.