I had this happen today, and was able to figure out that it was because of duplicate external boundary conditions in the unsteady flow file.
HEC-RAS isn’t always very good about making sure that the unsteady flow file matches the geometry. In my case, I had deleted the external BC to do something, then re-added them by copying them from another version of the model in RAS Mapper. When I pasted them in, it renamed them with generic names (BC Line 1, etc.). I then renamed two of the lines back to the original names.
When I deleted them, the original entries in the unsteady flow file didn’t get deleted, but when I renamed them, RAS didn’t check the file to see if there was a matching entry, so it added a second copy. When I deleted this extra copy from the file with Notepad, it fixed the problem.
Looking at the whole file, I think I need to do some cleanup, because there are other ‘orphan’ entries that don’t show up in the user interface because the BC locations have been deleted.