Curious indeed. I can reproduce this on xenial mounting a share from a
windows 7 enterprise VM:

With vers 2.1 (same with 2.0):
root@nsn7:~# l /c
total 3,0G
drwxr-xr-x  2 andreas andreas 4,0K Jun 12 16:58 .
drwxr-xr-x 33 root    root    4,0K Jun 27 15:56 ..
-rwxr-xr-x  1 andreas andreas   24 Jun 10  2009 autoexec.bat
-rwxr-xr-x  1 andreas andreas   10 Jun 10  2009 config.sys
drwxr-xr-x  2 andreas andreas 4,0K Out 23  2013 Documents and Settings
-rwxr-xr-x  1 andreas andreas 3,0G Jun 27 15:45 pagefile.sys
drwxr-xr-x  2 andreas andreas    0 Jul 13  2009 PerfLogs
drwxr-xr-x  2 andreas andreas    0 Jun 12 16:10 ProgramData
dr-xr-xr-x  2 andreas andreas    0 Jun 12 21:05 Program Files
drwxr-xr-x  2 andreas andreas    0 Out 23  2013 Recovery
drwxr-xr-x  2 andreas andreas    0 Nov 26  2014 System Volume Information
dr-xr-xr-x  2 andreas andreas    0 Out 23  2013 Users
drwxr-xr-x  2 andreas andreas    0 Out 23  2013 Wallpaper
drwxr-xr-x  2 andreas andreas    0 Jun 12 16:53 Windows
root@nsn7:~# mount|grep cifs
//10.0.7.128/c on /c type cifs 
(rw,relatime,vers=2.1,sec=ntlmssp,cache=strict,username=IEUser,domain=WORKGROUP,uid=1000,forceuid,gid=1000,forcegid,addr=10.0.7.128,file_mode=0755,dir_mode=0755,nounix,mapposix,rsize=1048576,wsize=1048576,actimeo=1)


Without the vers= parameter we get two extra directories: "Arquivos de 
Programas RFB" and "$Recycle.Bin":
root@nsn7:~# l /c
total 3,0G
drwxr-xr-x  2 andreas andreas 4,0K Jun 12 16:58 .
drwxr-xr-x 33 root    root    4,0K Jun 27 15:56 ..
drwxr-xr-x  2 andreas andreas    0 Jun 12 20:52 Arquivos de Programas RFB
-rwxr-xr-x  1 andreas andreas   24 Jun 10  2009 autoexec.bat
-rwxr-xr-x  1 andreas andreas   10 Jun 10  2009 config.sys
drwxr-xr-x  2 andreas andreas    0 Jul 14  2009 Documents and Settings
-rwxr-xr-x  1 andreas andreas 3,0G Jun 27 15:45 pagefile.sys
drwxr-xr-x  2 andreas andreas    0 Jul 13  2009 PerfLogs
drwxr-xr-x  2 andreas andreas    0 Jun 12 16:10 ProgramData
dr-xr-xr-x  2 andreas andreas    0 Jun 12 21:05 Program Files
drwxr-xr-x  2 andreas andreas    0 Out 23  2013 Recovery
drwxr-xr-x  2 andreas andreas    0 Out 23  2013 $Recycle.Bin
drwxr-xr-x  2 andreas andreas    0 Nov 26  2014 System Volume Information
dr-xr-xr-x  2 andreas andreas    0 Out 23  2013 Users
drwxr-xr-x  2 andreas andreas    0 Out 23  2013 Wallpaper
drwxr-xr-x  2 andreas andreas    0 Jun 12 16:53 Windows
# mount|grep cifs
//10.0.7.128/c on /c type cifs 
(rw,relatime,vers=1.0,cache=strict,username=IEUser,domain=WORKGROUP,uid=1000,forceuid,gid=1000,forcegid,addr=10.0.7.128,file_mode=0755,dir_mode=0755,nounix,serverino,mapposix,rsize=61440,wsize=65536,actimeo=1)


** Changed in: samba (Ubuntu)
       Status: New => Confirmed

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https://bugs.launchpad.net/bugs/1572132

Title:
  SMB driver (SMBv2) does not show all files when mounting a windows top
  level share

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