We were recently alerted to an issue where devices onboarded to Microsoft Defender for Endpoint are not properly reflected in the Microsoft Intune admin center report for devices with/without the Defender for Endpoint sensor. We've identified a bug that is causing incorrect counts for the number of devices onboarded to Defender for Endpoint and are working on a fix that is expected to be released later this year. The report is located under Endpoint security > Microsoft Defender for Endpoint and on the connector page.
Note: This is a reporting bug only. It does not impact onboarding to Defender for Endpoint.
Temporary workaround
As a temporary workaround, check for the Defender for Endpoint onboarding status in the Antivirus agent status report under Reports > Microsoft Defender Antivirus. Look for the columns for MDE Onboarding Status and MDE Sense Running State for more information.
We’ll update this post when the fix has rolled out or as more information becomes available. If you have any questions, let us know though comments on this post, or by tagging @IntuneSuppTeam on Twitter.