Hello,
I'm having a strange issue: I have a custom print service published from Pro to our federated server (Portal/Enterprise 10.8.1). When I use this custom print service in a web app built in the developer edition of WAB, the output captures the legend (and unfortunately includes all the features as opposed to only those in the map frame, which is a different issue...) but doesn't actually show the layers themselves in the map frame. See photos of an example zoning dataset. Stumped on this one - I've never had this problem with previous custom print services (published from ArcMap to a stand alone server).
I had the same issue. I found that only the map image layer was published, once the feature layer was published the print tool started working