I am having two issues with the spatial query on selected features.
1) Based on the query widget documentation, "Within" should result in all source features that are enclosed by the selected filter features. Mine is coming up empty even though there are source polygons that fall fully within the selected polygon.
2) "Intersect" is giving inconsistent answers based on how many features are selected in the filter layer. For example, if I have polygon A selected, it outputs the correct features from the source layer. If I have both polygon A and B selected, I'm noticing that some source layer features are incorrectly excluded.
I know that based on previous ExB questions, Esri staff may ask to replicate or further investigate the issue. I'm happy to provide more information if needed.
I am also having the same problem (and other similar ones) with the spatial queries in the query widget. None of the query types seem to correctly or consistently select the appropriate source data points - sometimes source data completely outside of the query area is selected, or sometimes incomplete source data is selected (such as half of the area that intersects a query feature, but not the other half). I am also happy to provide additional follow up info/documentation.
Thanks @DRicotta for your input! I am still having the same issues making it impossible to share this app with my organization. I posted another question here with more details and considerations that hopefully will be addressed by Esri.