This happens when Browse Projects and Create Issue Permission is given as "Application Access as Jira Software" (or Permissions not pertaining to roles/group) and does not have the "Set issue security permission"
Now to troubleshoot,
User is not in the any roles of the project.
Issue security scheme has default security level which is limited to less number of people.
When this user creates an issue, the issue is created but user will not be able to see it.
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