Paul,
There can be several reasons, including the one you mentioned. If you are new to Arc Hydro and have not done so yet, please review "Arc Hydro: Project Development Best Practices" (that and many other AH docs are linked at https://www.esri.com/en-us/industries/water-resources/arc-hydro). Few things to get out of the way. 1. Possible projection issues. Make sure your polygons are in the same projection as your flow direction raster (best practice - have a feature dataset that has the same SR as your raster data and load your polygons into it and then use it as input to the tool). 2. Resolution of the DEM compared to the size of the polygon. If your polys are small compared to the fdr/dem cell size, you can get strange results. Solution is to use finer resolution DEM (and corresponding fdr derived from it). 3. "Strange" fdr. Was fdr developed from hydro-conditioned DEM? If not, your fdr can return "nothing" when doing watershed analysis (there is no contributing area).
One thing you can try is to isolate one of the polygons that did not succeed (copy it into its own FC), and run the tool just on that one poly. If it does not work, then try to do the process by hand:
1. convert polygon to raster (make sure you correctly specify environment for cell size, raster snapping, and extent to the one of fdr).
2. run Spatial Analyst watershed function using polygon raster representation from #1 and fdr as inputs.
If that does not return expected results (it will be a raster), then "you have a problem", most likely with fdr of polygon size.
Hope this helps.
Dean
