The Select by Location tool does not select the extruded points.
Last Published: February 17, 2015ArcGIS for Desktop
Bug ID Number
February 10, 2015
November 24, 2020
ArcGIS for Desktop
Operating System Version
After review by the development team, it has been determined that this issue is related to a known limitation with the software that lies outside of Esri's control. The issue's Additional Information section may contain further explanation.
This is as designed. Select by Location uses the geometry of the feature, extrusion is just a visual representation of the geometry.
1. Convert the extruded features to multipatch using the Layer 3D to Feature Class tool.
2. Use this mulitpatch instead of the point2D in the Select by Location tool.