After disabling coexistence mode within a Virus and Spyware Protection (Endpoint Protection) or Malware Protection (Endpoint Security) policy, Windows Defender is not disabled as expected.
Windows Defender Tamper Protection is enabled.
Note: as of Windows 10 1903 SEP no longer disables Defender as result of Microsoft changes, further details:
Endpoint Protection No Longer Disables Windows Defender On Some Windows 10 Computers
When disabling co-exist mode, the Endpoint Protection/Security agent is unable to disable Windows Defender if Windows Defender Tamper Protection is enabled because Windows Defender Tamper Protection blocks the action.
To allow the Endpoint Protection/Security agent to disable Windows Defender when disabling coexistence mode, Windows Defender Tamper Protection must be disabled. Alternatively, Windows Defender can be disabled manually.