ee-specific-lines-check failed to rebase when CE branch is not up-to-date with CE master

Original title: ee-files-location-check "git status not clean" - after merging master back into CE branch:

I merged EE master back into my EE branch, and CE master back into my CE branch.

• CE-MR: https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/18790
• EE-MR: https://gitlab.com/gitlab-org/gitlab-ee/merge_requests/5601
• Failing Job: https://gitlab.com/gitlab-org/gitlab-ee/-/jobs/67424027

Now I get this error:

=> Running `git rebase --onto e960931828b85205f2355c6040ec48ca14740e48 e960931828b85205f2355c6040ec48ca14740e48~1 target-ce/5710-add-contact-sales-option-for-epics`
.git/rebase-apply/patch:1350: trailing whitespace.
- [ ] Label your MR with the ~security label, prefix the title with `WIP: [master]`   
.git/rebase-apply/patch:1405: trailing whitespace.
/label ~security 
.git/rebase-apply/patch:1476: trailing whitespace.
Closes 
.git/rebase-apply/patch:1690: trailing whitespace.
env: 
.git/rebase-apply/patch:1691: trailing whitespace.
  - SKIP_STORAGE_VALIDATION=true 
warning: squelched 796 whitespace errors
warning: 801 lines add whitespace errors.
warning: Cannot merge binary files: vendor/project_templates/spring.tar.gz (HEAD vs. Merge branch 'tz-optimize-emoji-sprite' into 'master')
warning: Cannot merge binary files: vendor/project_templates/rails.tar.gz (HEAD vs. Merge branch 'tz-optimize-emoji-sprite' into 'master')
warning: Cannot merge binary files: vendor/project_templates/express.tar.gz (HEAD vs. Merge branch 'tz-optimize-emoji-sprite' into 'master')
error: Failed to merge in the changes.
=> Running `git status --porcelain`

💥 Git status not clean! This shouldn't happen. Please create an issue
💥 and ping @godfat to investigate.

⚠️ Git status:

AA .flayignore
AA .gitignore
AA .gitlab/issue_templates/Security Developer Workflow.md
[... hundreds of lines]
AA yarn.lock