This is that folder how it should be so, if there are no errors while uncompressing, the MDT Bundle used is not complete.
Could you please check if the missing folders are mentioned in the uncompression log?
If not, could you please check your MDT Bundle folder MDTBundle\Content\Deploy (from the folder it has been imported from or the file in the folder “\wwwrootbes\Uploads\8348A51…” on your bigfix main server)? If it’s also missing the folders in my screenshot, it has not been correctly created in the first case (the original creation dir), created or imported in the second case (the folder in the Uploads dir).
After checking this, we can define next step (e.g. if to recreate the MDT Bundle, or re-import it, etc.)