Everything below the top level work item needs a parent for the backlog structure to work correctly. So as you create new work items, everyone should keep an eye on that. ScrumMasters should facilitate their teams backlog work and monitor their Backlogs for data quality problems like these.
Some info on the VSTS Work Item Visualization extension, providing some quick tips and links to learn more. This VSTS extension allows you to visualize relationships between work items from within the work item form.