I'm having the same issue - I'm using the Side Accordion Storytelling template to display three different maps that are filtered versions of the same service. When viewing the maps on the ArcGIS.com map viewer, the filters work as expected, limiting the visibility of features based on my created expressions while ALSO hiding the info pop-ups of those hidden features. That is to say, if you click on the location of a feature hidden using the filter, the hidden feature's info pop-up will not appear.
However, once these maps are displayed using the Side Accordion storytelling template, the features remain visibly hidden, but the info pop-ups will open if you click on the location of the hidden features.
So if I have multiple features stacked on top of each other (or if they are located very close to each other), clicking on a filtered visible feature will also open the info pop-ups for all of the hidden features.