Steps to reproduce:

# docker-compose.yml
version: '3'
services:
    jenkins:
        image: jenkins/jenkins:2.277
        ports:
            - 8080:8080

$ docker-compose up

• Unlock Jenkins
• Install suggested plugins
• Create a user
• Create a public repository on GitHub with the following Jenkinsfile in the master branch:

  pipeline {
      agent any
      stages {
          stage('Stage 1') {
              steps {
                  sh 'echo $GIT_COMMIT'
              }
          }
      }
  }
  

• https://github.com/USER/REPO/settings/hooks
  • Add webhook
  • Payload URL: $JENKINS_BASE_URL/github-webhook/ (trailing slash is important)
  • Add webook
• Manage Jenkins > Manage Credentials > (Jenkins/global) > Add credentials
  • Kind: Username with password
  • Scope: System
  • Username: (email)
  • Password: (password)
• New Item
  • Enter an item name
  • Pipeline
  • OK
  • Check GitHub project
  • Enter the URL: https://github.com/REPO/NAME
  • Check GitHub hook trigger for GITScm polling
  • Pipeline: Pipeline from SCM
  • SCM: Git
  • Repository URL: https://github.com/REPO/NAME
  • Credentials: (credentials)
  • Branch specifier: */master (the default)
  • Save
• Build Now (to make GitHub plugin work)

$ n=a; echo "$n" > "$n"; git add "$n"; git commit -m "$n"
$ git push origin HEAD

It built the pushed commit (a).

$ git checkout -b master2
$ n=b; echo "$n" > "$n"; git add "$n"; git commit -m "$n"
$ git push origin HEAD

The build hasn't started (as expected).

• Configure > Pipeline > Branches to build
  • Branch specifier: */master*
  • Save

$ git checkout master
$ n=c; echo "$n" > "$n"; git add "$n"; git commit -m "$n"
$ git push origin HEAD

The build has started but it builds commit b, not c.

$ n=d; echo "$n" > "$n"; git add "$n"; git commit -m "$n"
$ git push origin HEAD

And now it built c and d.