I believe I've come across a bug which stops pop-ups working properly in story maps.
The issue I've found is sometimes the pop-ups stop working for some reason and I believe this is the cause.
So in the Moorings or Marine Farms tabs you can click on the marine farm or mooring point and get a pop up. If you leave the pop-up window open and pan the map so the pop-up disappears off the side of the screen, you then don't get the pop-up on any other features until you zoom in or out on the map.
I've tried this in Chrome, Firefox and IE11 and get the same thing happening.
I also get the pop-up stop working if I select a feature, close the pop up and then pan to another part of the map and try select another feature.
The features are drawing from two map services, with pop-ups configured in an AGOL webmap.
If the data is added as a single layer from a map service e.g. in the Foreshore structure tab which comes from then this issue doesn't occur. Its only when the whole map service is added to the map and popups configured on layers within the map service that this seems to happen.