I'm seeing this with a dashboard that I just authored. It has two map services from ArcGIS for Server and a feature service from ArcGIS for Server. The web map legend shows both the map service items and nothing from the feature services. The Operations Dashboard legend widget only shows the first (lowest) map service layer. If I hide the legend item for the first layer, no legend items show up in the dashboard.
Do the layers have scale dependencies so that they only draw in certain scale ranges? I just noticed that the layers missing from my legend are the ones that do not draw at smaller scales. I wonder if the legend is created when the Operations Dashboard loads and not updated when the zoom level changes.