We've just got a similar for our attempt on our test environment
We ran the CMD as adminstrator
OSError: [WinError 145] The directory is not empty: 'C:\\Users\\ADEB3D~1\\AppData\\Local\\Temp\\tmpw8tj9mrg\\org\\apache\\logging\\log4j\\core'
We ran the list again afterwards it patched the first 1 of 5 but not the
D:\ArcGIS\Server\framework\lib\shared\log4j-core-2.8.2.jar -- patched
D:\ArcGIS\Server\tools\configurebasedeployment\lib\log4j-core.jar -- needs patching
D:\ArcGIS\Server\tools\createsite\lib\log4j-core.jar -- needs patching
D:\ArcGIS\Server\tools\upgradebasedeployment\lib\log4j-core.jar -- needs patching
D:\ArcGIS\Server\tools\upgradeserver\lib\log4j-core.jar -- needs patching
Anyone got any suggestions?