Windows Defender scans are skipping files due to a configured exclusion or network scanning setting. Users who report receiving these messages, though, do not have any exclusions configured in the Windows Defender preferences. The issue has been happening since around March 10th, 2020, which coincides with the March Patch Tuesday. BleepingComputer has contacted Microsoft about the bug but has not heard back at this time. There appears to be no common denominator that can be seen in affected users. The bug is being reported under different Antimalware Client versions and does not affect everyone running the same engine version.
Source: https://www.bleepingcomputer.com/news/microsoft/windows-defender-bug-in-windows-10-skips-files-during-scans/