We are using ArcGIS 10.3.1 to create map services to publish on ArcGIS Portal also 10.3 (I think). Some of these are created as Map Images as the layers within them need to be kept together. The layers are grouped within ArcMap and some have sub-groups. All the data shows in the Web Map but when the Web Map is used in a Web App, those lars in sub groups don't show and/ or don't work properly with pop-ups not working etc.
Can sub groups be used in Web Apps and if so, how do I get them to work?
Make sure you turn ON all the Group/Subgroup layers in the Table of Contents of ArcMap before publishing your map. You may choose to uncheck the individual layers within them, if desired.
I hope this solves the pop-up issue...