Squash and merge fails with a trailing whitespace error

Internal Zendesk ticket: https://gitlab.zendesk.com/agent/tickets/83087

A customer is getting the following error in the githost.log when attempting a Squash and Merge, and I think it's a bug:

September 27, 2017 13:32 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!36): Failed to apply patch with `/opt/gitlab/embedded/bin/git diff --binary 174bd57ac467209359a357011563aee512d7a5de...90d259b29be69ebea1d87aa1b4510025a813fc4c | /opt/gitlab/embedded/bin/git apply --index`: 
September 27, 2017 13:32 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!36): <stdin>:212: trailing whitespace. 
September 27, 2017 13:32 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!36): Failed to apply patch with `/opt/gitlab/embedded/bin/git diff --binary 174bd57ac467209359a357011563aee512d7a5de...90d259b29be69ebea1d87aa1b4510025a813fc4c | /opt/gitlab/embedded/bin/git apply --index`: 
September 27, 2017 13:32 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!36): <stdin>:212: trailing whitespace. 
September 26, 2017 13:50 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!37): Failed to apply patch with `/opt/gitlab/embedded/bin/git diff --binary 3d6ed609d6120dbec142ce1f8f24682dbf30e7b5...6d12a069138bd7b6450defcf1d77a7ba0a8e492d | /opt/gitlab/embedded/bin/git apply --index`: 
September 26, 2017 13:50 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!37): error: patch failed: pom.xml:68 
September 26, 2017 13:50 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!37): Failed to apply patch with `/opt/gitlab/embedded/bin/git diff --binary 3d6ed609d6120dbec142ce1f8f24682dbf30e7b5...6d12a069138bd7b6450defcf1d77a7ba0a8e492d | /opt/gitlab/embedded/bin/git apply --index`: 
September 26, 2017 13:50 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!37): error: patch failed: pom.xml:68 
September 26, 2017 13:51 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!37): Failed to apply patch with `/opt/gitlab/embedded/bin/git diff --binary 3d6ed609d6120dbec142ce1f8f24682dbf30e7b5...6d12a069138bd7b6450defcf1d77a7ba0a8e492d | /opt/gitlab/embedded/bin/git apply --index`: 
September 26, 2017 13:51 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!37): error: patch failed: pom.xml:68 
September 26, 2017 13:53 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!37): Failed to apply patch with `/opt/gitlab/embedded/bin/git diff --binary 3d6ed609d6120dbec142ce1f8f24682dbf30e7b5...6d12a069138bd7b6450defcf1d77a7ba0a8e492d | /opt/gitlab/embedded/bin/git apply --index`: 
September 26, 2017 13:53 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!37): error: patch failed: pom.xml:68 
September 25, 2017 15:47 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!33): Failed to apply patch with `/opt/gitlab/embedded/bin/git diff --binary 8fd82462f6537e48975f19ad5e6a3a5ca07f0423...bc5e8f873111de999504932575526ca6ab208d47 | /opt/gitlab/embedded/bin/git apply --index`: 
September 25, 2017 15:47 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!33): <stdin>:335: trailing whitespace. 
September 25, 2017 15:49 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!33): Failed to apply patch with `/opt/gitlab/embedded/bin/git diff --binary 8fd82462f6537e48975f19ad5e6a3a5ca07f0423...bc5e8f873111de999504932575526ca6ab208d47 | /opt/gitlab/embedded/bin/git apply --index`: 
September 25, 2017 15:49 -> ERROR -> MergeRequests::SquashService error (<group>/<project>!33): <stdin>:335: trailing whitespace

The customer is running 9.5.4-ee

/cc @victorwu