When I put the CU Files of the May 2016 CU for SharePoint 2016 into the update folder, they are not applied. This is due to the naming convention, which seems to have changed. I have the following files in the CU:
sts2016-kb3115088-fullfile-x64-glb.exe
wssloc2016-kb2920690-fullfile-x64-glb.exe
Comments: ** Comment from web user: owarya **
sts2016-kb3115088-fullfile-x64-glb.exe
wssloc2016-kb2920690-fullfile-x64-glb.exe
Comments: ** Comment from web user: owarya **
+1 this.
sts2016-kb3115181-fullfile-x64-glb.exe (June 2016) was also ignored. Installed it manually during the pause after SharePoint binary installation.