Disk System Info does not match du, df, and ncdu

Summary

Disk info shown on /admin/system_info does not match du, df, and ncdu

Steps to reproduce

Install GitLab Omnibus 8.11.2 on RHEL 6.7
Configure for Git data to be stored on secondary volume
Install lots of Git data
Run sudo du -sch, sudo df -h, ncdu and compare results to /admin/system_info

Expected behavior

I expect /admin/system_info to output accurate disk data

Actual behavior

The total disk space shown on /admin/system_info is accurate however the used disk space shown is ~13% larger than du, df, and ncdu.

~~I also have one disk shown with 0 bytes/0 bytes data that is not shown with df and should probably be excluded from the view.~~ -> MR at https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/9355

Output of checks

Results of GitLab application Check

All good

Results of GitLab environment info

System information
System:
Current User:   git
Using RVM:      no
Ruby Version:   2.3.1p112
Gem Version:    2.6.6
Bundler Version:2.3.0
Rake Version:   10.5.0
Sidekiq Version:4.1.4

GitLab information
Version:        8.11.2
Revision:       e618ce2
Directory:      /opt/gitlab/embedded/service/gitlab-rails
DB Adapter:     postgresql
URL:            https://company.com
HTTP Clone URL: https://company.com/some-group/some-project.git
SSH Clone URL:  git@company.com:some-group/some-project.git
Using LDAP:     no
Using Omniauth: yes
Omniauth Providers: saml

GitLab Shell
Version:        3.4.0
Repository storage paths:
- default:      /app/gitlab/git-data/repositories
Hooks:          /opt/gitlab/embedded/service/gitlab-shell/hooks/
Git:            /opt/gitlab/embedded/bin/git

Links

/cc @joshfng @vsizov @smcgivern