The concept of NextDownID (NDID) is fairly straightforward (HydroID of the downstream feature in the same feature class). For catchments, it is based on drainage line connectivity and relationship between catchment and its drainage line. It is hard to tell what might be going on with the process based on just the picture you provided (without HydroID and DrainID attributes on catchments and drainage lines surrounding the problem area). I run the standard terrain processing workflow (although i did fill sinks) using 3.2.52 build, and the catchment NDIDs look good. There are few ways to check what is going on on your end, but the simplest way is for you to send me the geodatabase with your processed vector data - at least drainage lines, catchments, adjoint catchments and APUNIQUEID table. I can quickly look at it and and see it anything pops out. If not, i might ask you to send the DEM and step-by-step process you went through and we'll try to see if we can recreate the problem with your data.
Dean