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Tiny, Illegitimate Watersheds created by Watershed Tool

Question asked by collinser on Jun 12, 2013
Latest reply on Jun 20, 2013 by SWalbridge-esristaff
I have recently been trying to delineate watersheds for several thousand points in my study area. To accomplish this, I have written a simple script tool that that takes a point shapefile, flow direction raster, and flow accumulation raster as inputs.  Essentially, the tool follows these steps: select point, snap pour point, delineate watershed, convert watershed raster to polygon, append polygon to a shapefile.  I'm overall pleased with the results, however, the tool seems to have generated about 200 more watersheds than it should have.  These "watersheds" are all about the same size (typically just one pixel) and fall along the edges of the larger legitimate watersheds (I have attached a map to help clarify this).  My data are all in the same state plane projection and the processing extent was set to match the flow direction raster I was using. 
Has anyone ever seen this problem when running the Watershed tool?  Are there any suggestions to prevent them from being generated?  The biggest problem they create for me is that they desynchronize the point IDs and the watershed IDs.  I could simply delete the illegitimate watersheds, but that doesn't really help me associate the points to their respective watershed.  Any help would be greatly appreciated.  Let me know if anything needs more explaining.

Thanks,
E
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