The duplicate finder works fine when there are two files input for comparison. But I cannot get it to identify duplicates in the same file. Am I doing something wrong or is the software not designed to do this?
If you mean trying to find things like two lines that are the same in a text file then no; the Duplicate Finder is not designed to do that.
It's meant to find two or more files that are the same but may have different names or/and are in different locations (file copies).
If you are looking for duplications within one file then you need a different tool for that.