Jenkins multibranch pipeline is unable to detect a branch from github

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I'm using multibranch pipeline for my github repo which polls the github repo for changes but it is unable to identify a branch. I have tried manually scanning the repo as well(using Scan Repository Now). When I checked the log of repository scan found that it is skipping the branch without any reason/error.

Repository Scan Log: See branch - PH055018

Started by user unknown or anonymous
[Tue Sep 18 01:48:11 CDT 2018] Starting branch indexing...
01:48:12 Connecting to https://github.***.com/api/v3 using admin/****** (GitHub Enterprise)
01:48:12 Connecting to https://github.***.com/api/v3 using admin/****** (GitHub Enterprise)
Examining Org/Branch1

  Checking branches...

  Getting remote branches...

    Checking branch AO055200

  Getting remote pull requests...
      ‘Jenkinsfile’ found
    Met criteria
No changes detected: AO055200 (still at 4591b6532f66cb042f577a010b15920d88228be4)

    Checking branch CR017933
      ‘Jenkinsfile’ found
    Met criteria
No changes detected: CR017933 (still at 3adf73afbdac409122f8094bb613dfaf2e5ccf20)

    Checking branch PH055018

    Checking branch master
      ‘Jenkinsfile’ found
    Met criteria
No changes detected: master (still at 76ffdb47caf9a544b1b19b4eb35d5b2df5fab77b)

  4 branches were processed

  Checking pull-requests...

    Checking pull request #29
      ‘Jenkinsfile’ found
    Met criteria
No changes detected: PR-29 (still at aca8973b0b496292c1342dbf63bab25fec0f068e+76ffdb47caf9a544b1b19b4eb35d5b2df5fab77b)

  1 pull requests were processed

Finished examining Org/Branch1

[Tue Sep 18 01:48:15 CDT 2018] Finished branch indexing. Indexing took 3.6 sec
Finished: SUCCESS

Jenkins has identified only 3 out of 4 branches even though all 4 branches have the JenkinsFile. Could anyone tell how do I debug this scenario?

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