Select by location Geoprocessing tool with processing extent not working

[SenthilKannan]

I wanted to select spatially intersected features between two feature classes but with in a restricted extend. So in environment setting>processing extent in the place of default I changed option to same as display. Output came as all intersected features not only for my display extent can some one can help me on this.  

[KoryKramer]

This would be a better question for the Geoprocessing‌ space.  

Providing more information and screenshots will also help get to solution faster.  e.g. are you working with points, lines, polygons?  Can you include screenshots of the data and the tool's settings?

Have you checked spatial indexes?