This happens because manual jobs are considered optional, and do not need to run.

Internally, manual jobs have allow_failure set to true by default, which means that these skipped manual jobs do not cause a pipeline failure. The YAML code below demonstrates how to write the manual job, which results in the same behavior. The job doesn't automatically start, is skipped, and the pipeline passes.

stages:
  - stage1
  - stage2

job1:
  stage: stage1
  script:
    - echo "this is an automatic job"

manual_job:
  stage: stage2
  script:
    - echo "This is a manual job"
  when: manual
  allow_failure: false

You can set allow_failure to true for any job, including both manual and automatic jobs, and then the pipeline does not care if the job runs successfully or not.