Spatial Join Returning Incorrect Counts of Points in Joint_Count Field

[BrettJenkinson]

I have been trying and failing to complete a spatial join in order to obtain total counts for different point data contained within different hosted feature layers, across 600+ different polygons that they fall within. There are three layers of point data I need to obtain counts for for each polygon. I keep getting incorrect counts returned to me. Does anyone have any idea the correct method or remedy to fix? 

[MichaelVolz]

Can you try to download the hosted layer to your machine and try the same process to see if you get the expected results, just as a test?9

[BrettJenkinson]

Michael,

I will attempt this later today. 

[SamSzotkowski]

I second the recommendation to download the hosted data and try there.  I've had one or two occasions in the past where the spatial index was stale or inaccurate somehow and my spatial joins were giving incorrect results until I recalculated the spatial index or copied the features into a new feature class.