Error during deployment: Application app is missing web.config file.

I'm getting below error.
Error during deployment: Application app is missing web.config file.
I have downloaded the zip file from the beanstalk , i noticed that there is app folder got created under main zip and app folder has the contents which includes web.config file as well. How do i prevent publish task to put the contents under main zip then putting under app folder?

Here is the command for publish:

--configuration $(BuildConfiguration) --output $(Build.StagingDirectory)\$(Build.BuildNumber).zip

under beanstalk task:
Published Application Path : $(Build.StagingDirectory)\$(Build.BuildNumber).zip

Start by reviewing the publish command and the Beanstalk task's Published Application Path to trace how the ZIP contents are packaged and consumed. Reproduce the nested app directory layout and verify that the deployment package places web.config at the expected application root.

Written by the indexing model from the issue text.