Difference not recognized correctly when resolving merge conflicts

Summary

When resolving merge conflicts online in gitlab, sometimes the use ours and use theirs buttons are not shown, and as the changes seem not to be recognized. It can even differ for files in one merge request.

Steps to reproduce

I can't determine why it works for some files and doesn't for others.
I tried reproducing it with the not working files in a new gitlab.com repository and it works there.

Example Project

See above

What is the current bug behavior?

When resolving merge conflicts in the gitlab webui, the buttons for use ours and use theirs are not shown for all files.

What is the expected correct behavior?

When there is a diff in the file, the buttons the choose the version for resolving the conflict should always be shown.

Relevant logs and/or screenshots

Results of GitLab environment info

 System information
System:         Ubuntu 16.04
Current User:   git
Using RVM:      no
Ruby Version:   2.4.4p296
Gem Version:    2.7.6
Bundler Version:1.16.2
Rake Version:   12.3.1
Redis Version:  3.2.11
Git Version:    2.17.1
Sidekiq Version:5.1.3
Go Version:     unknown

GitLab information
Version:        11.0.3
Revision:       aa62075
Directory:      /opt/gitlab/embedded/service/gitlab-rails
DB Adapter:     postgresql
URL:            http://xxxx.xxxx.de
HTTP Clone URL: http://xxxx.xxxx.de/some-group/some-project.git
SSH Clone URL:  git@xxx.de:some-group/some-project.git
Using LDAP:     yes
Using Omniauth: no

GitLab Shell
Version:        7.1.4
Repository storage paths:
- default:      /var/opt/gitlab/git-data/repositories
Hooks:          /opt/gitlab/embedded/service/gitla``b-shell/hooks
Git:            /opt/gitlab/embedded/bin/git

Results of GitLab application Check

Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Check GitLab API access: OK
Redis available via internal API: OK

Access to /var/opt/gitlab/.ssh/authorized_keys: OK
gitlab-shell self-check successful

Checking GitLab Shell ... Finished

Checking Sidekiq ...

Running? ... yes
Number of Sidekiq processes ... 1

Checking Sidekiq ... Finished

Reply by email is disabled in config/gitlab.yml
Checking LDAP ...

Server: ldapmain
LDAP authentication... Success
LDAP users with access to your GitLab server (only showing the first 100 results                                                         )
xxx
Checking LDAP ... Finished

Checking GitLab ...

Git configured correctly? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config up to date? ... yes
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory exists? ... yes
Uploads directory has correct permissions? ... yes
Uploads directory tmp has correct permissions? ... yes
Init script exists? ... skipped (omnibus-gitlab has no init script)
Init script up-to-date? ... skipped (omnibus-gitlab has no init script)
Projects have namespace: ...
3/1 ... yes
3/3 ... yes
3/5 ... yes
3/6 ... yes
3/7 ... yes
3/9 ... yes
14/10 ... yes
3/11 ... yes
18/12 ... yes
3/13 ... yes
19/14 ... yes
3/15 ... yes
3/16 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.3.5 ? ... yes (2.4.4)
Git version >= 2.9.5 ? ... yes (2.17.1)
Git user has default SSH configuration? ... yes
Active users: ... 23

Checking GitLab ... Finished