When searching specifically for a file type in Alfred's filter, it will be setting the file content type in the mdfind query (and the scope you have set). The mdfind you are doing searches your entire drive for all file types then grep through for the file types (which may not contain the correct metadata). This will potentially match more...
Could you share your file filter workflow so I can take a look. Also, are the files not being found inside your search scope, if so, can you do an mdls on one of those files to check the kMDItemContentType.
Cheers,
Andrew