Sorry about your issues, it can be tricky and we are working on providing proper guideline in the builder so it should not be a problem anymore soon. Here is the first set of rules to works well if the application you are trying to embed in your main story is public:
- if your application is accessed over https it can only include other applications over https
- if your application is accessed over http it can include other applications over http or https
It does not matter much if the main story is public or not but if the application you are trying to embed is not public there is one more rule that depend on your organization configuration and your browser: as the application is not public, the application may try to redirect to ArcGIS Online sign-in page over HTTPS which most browser except Internet Explorer will refuse as it's a change in protocol. The browser unfortunately won't notify the app or display any error message.
I believe you must be in that case. Can you make the embedded application public (also make sure all of it's content is public)? If you can't that's ok and loading your story over HTTPS should fix the issue in most case.
The same pattern should apply for webscene that are hosted in ArcGIS Online. Web scene that are hosted on Portal for ArcGIS can't be embedded in other application by default. To enable this, a configuration on the Portal webserver need to be performed. As far as I know there is no documentation about this and I am not sure this is fully supported so I suggest that you contact Esri Technical support if this is your case, see Esri Support
Note that My Stories | Story Maps can help you diagnose if all the content of your are sharing at the level you expect.
