This problem occurs when coverage of the same code from separate builds is merged. Multiple coverage files of identical code, when merged, will show duplicate assemblies if the build is not the same in each coverage file.

The underlying issue is the doc IDs, which are assigned when the build takes place and used by NCover to identify all the code elements. The doc IDs are different in every build -- even for the same code -- so assemblies that appear otherwise identical are still different to the NCover profiler.