Bug
The Intersect tool in ArcGIS Pro fails to generate output and returns the warning messages “WARNING 000117: empty output generated” and “WARNING 000953: Extent of the overlay operation will be empty.” when using two polygon layers from a GeoPackage (.gpkg) if the input layers are added from the Contents pane instead of the Catalog pane despite valid overlapping geometries and matching CRS.
| Bug ID Number | BUG-000181025 |
|---|---|
| Submitted | November 17, 2025 |
| Last Modified | December 4, 2025 |
| Applies to | ArcGIS Pro |
| Version found | 3.5.2 |
| Operating System | Windows OS |
| Operating System Version | 11.0 64 bit |
| Status | In Product Plan |
Workaround
The issue does not occur when the input layers are added from the Catalog pane instead of the Contents pane. Drag the polygon layers directly from Catalog > Databases > [GeoPackage] into the Intersect tool input. The Intersect tool processes the GeoPackage layers correctly and produces the expected output.
Steps to Reproduce
Bug ID: BUG-000181025
Software:
- ArcGIS Pro
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