Recently we ran into an issue when adding a node into Windows 2016 Cluster.
The validation test succeeded with no issues but as soon as the join process has initiated we were hit with the following error “Keyset does not exist 0x80090016″
After looking into the issue we discovered that the permission on the node in questions were incorrect on the C:\ProgramData\Microsoft\Crypto\RSA\MachineKeys directory.
We reset the permissions of the folder back to default, as found here https://support.microsoft.com/en-gb/help/278381/default-permissions-for-the-machinekeys-folders
We then tried to readd the node and it succeeded with no issues.