This thread is a but old now but i am running into this same issue with ArcMap 10.8.1. I have tried re-downloading hydrotools from https://downloads.esri.com/archydro/archydro/Setup/10.8/10.8.0.33/
and my DEM comes from SRTM (.hgt) files. The Solution proposed by christine seems to take me back to an older version of Hydrotools and I also tried Mark's solution and ensured my streams layer (downloaded from WWF hydrosheds) has unique study id's.
Any help would be greatly appreciated