Without more precise information, I would guess this is happening because you are importing from multiple shares from your NAS, which contain redundant portions of the directory tree. Don't do that. If MC finds a file at two different locations, they are considered two different files.
An example, showing the partial directory structure of each share:
Share1: (\\ROOT)
\Root
|-\All Movies
|-\HD Movies
|-\SD Movies
|-\New Movies
Share2: (\\NEWMOVIES)
\Root\All Movies\New Movies
So let's say you put Batman in a folder under New Movies. Now let's say you run an import of \\NEWMOVIES and then run an import of \\ROOT
MC will see Batman twice:
\\ROOT\All Movies\New Movies\Batman\Batman.mkv
\\NEWMOVIES\Batman\Batman.mkv
If that is your problem, don't run imports from shares that are subdirectories of higher level shares you are also importing.
You can cause the same effect by mounting shares as different drive letters if they let you access the same files. F:\Batman\Batman.mkv is considered a different file from G:\Batman\Batman.mkv
MC uses the full file name, including the path, to uniquely identify files. You will confuse that process if you make the same file have multiple paths, and try to import them all.