Rebase not working

Summary

Rebase button on Merge Request does nothing or seems to do nothing.

Customer request at https://gitlab.zendesk.com/agent/tickets/42703

Steps to reproduce

On project settings use Merge commit with semi-linear history for merge method.
Branch out of master branch-a
Make a new commit on master
Make a new commit on branch-a (different file)
Push to branch-a
Open an MR from branch-a to master
the MR ask to rebase before merging. Press the Rebase onto master button
Wait for the spinner to stop and everything seems to be on the same state as before with the rebase button still available.

Expected behavior

When FF is not possible I get the following message:

Fast-forward merge is not possible. Rebase the source branch onto the 
target branch or merge target branch into source branch to allow this 
merge request to be merged.

After clicking on the Rebase button I expect the MR to be available for merging.

Actual behavior

After clicking the Rebasebutton I don't see any change in the MR's status. The message is still the same.

Relevant logs and/or screenshots

https://app.hyfy.io/v/abA4UUO7t5/

Output of checks

Results of GitLab application Check

Checking GitLab Shell ...

GitLab Shell version >= 3.6.1 ? ... OK (3.6.1)
Repo base directory exists?
default... yes
Repo storage directories are symlinks?
default... no
Repo paths owned by git:git?
default... yes
Repo paths access is drwxrws---?
default... yes
hooks directories in repos are links: ...
5/1 ... ok
4/2 ... ok
3/3 ... ok
5/4 ... ok
11/5 ... ok
11/6 ... ok
6/7 ... ok
6/8 ... ok
11/9 ... ok
11/10 ... ok
6/11 ... ok
5/12 ... ok
5/13 ... ok
11/14 ... ok
5/16 ... ok
5/19 ... ok
5/20 ... ok
5/21 ... ok
6/22 ... ok
6/23 ... ok
6/24 ... ok
6/25 ... ok
4/26 ... ok
5/27 ... repository is empty
5/28 ... repository is empty
5/29 ... repository is empty
5/30 ... repository is empty
20/31 ... ok
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Check GitLab API access: OK
Access to /var/opt/gitlab/.ssh/authorized_keys: OK
Send ping to redis server: OK
gitlab-shell self-check successful

Checking GitLab Shell ... Finished

Checking Sidekiq ...

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

Checking Sidekiq ... Finished

Checking Reply by email ...

Reply by email is disabled in config/gitlab.yml

Checking Reply by email ... Finished

Checking LDAP ...

LDAP is disabled in config/gitlab.yml

Checking LDAP ... Finished

Checking GitLab ...

Git configured with autocrlf=input? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config outdated? ... no
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory setup correctly? ... no
  Try fixing it:
  sudo chown -R git /var/opt/gitlab/gitlab-rails/uploads
  sudo find /var/opt/gitlab/gitlab-rails/uploads -type f -exec chmod 0644 {} \;
  sudo find /var/opt/gitlab/gitlab-rails/uploads -type d -not -path /var/opt/gitlab/gitlab-rails/uploads -exec chmod 0700 {} \;
  For more information see:
  doc/install/installation.md in section "GitLab"
  Please fix the error above and rerun the checks.
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: ...
5/1 ... yes
4/2 ... yes
3/3 ... yes
5/4 ... yes
11/5 ... yes
11/6 ... yes
6/7 ... yes
6/8 ... yes
11/9 ... yes
11/10 ... yes
6/11 ... yes
5/12 ... yes
5/13 ... yes
11/14 ... yes
5/16 ... yes
5/19 ... yes
5/20 ... yes
5/21 ... yes
6/22 ... yes
6/23 ... yes
6/24 ... yes
6/25 ... yes
4/26 ... yes
5/27 ... yes
5/28 ... yes
5/29 ... yes
5/30 ... yes
20/31 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.1.0 ? ... yes (2.3.1)
Your git bin path is "/opt/gitlab/embedded/bin/git"
Git version >= 2.7.3 ? ... yes (2.7.4)
Active users: 9

Checking GitLab ... Finished

(we will only investigate if the tests are passing)

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:1.13.1
Rake Version:	10.5.0
Sidekiq Version:4.1.4

GitLab information
Version:	8.12.4-ee
Revision:	c810497
Directory:	/opt/gitlab/embedded/service/gitlab-rails
DB Adapter:	PostgreSQL
DB Version:	9.2.18
URL:		https://gitlab.domain.tld
HTTP Clone URL:	https://gitlab.domain.tld/some-group/some-project.git
SSH Clone URL:	ssh://git@gitlab.domain.tld:10022/some-group/some-project.git
Elasticsearch:	no
Geo:		no
Using LDAP:	no
Using Omniauth:	yes
Omniauth Providers: saml

GitLab Shell
Version:	3.6.1
Repository storage paths:
- default: 	/var/opt/gitlab/git-data/repositories
Hooks:		/opt/gitlab/embedded/service/gitlab-shell/hooks/
Git:		/opt/gitlab/embedded/bin/git

Possible fixes

(If you can, link to the line of code that might be responsible for the problem)

/cc @dbalexandre any ideas on this?