Cannot copy and paste files over SMB but works on AFP
This has been resolved by upgrading the server to El Capitan. Copy and paste files on the sharepoint works now when accessing from MacBooks and iMacs running El Capitan.

Upgrade note, I find the order of steps for the upgrade important. The following are what I find the shortest and easiest steps when done in that order:


Backup. (I used Time Machine, but use whatever works for you.)
Run Install El Capitan.app, I had it saved to the local disk, otherwise run it from the Mac App Store.
Log back in after the upgrade has rebooted the server.
Run all El Capitan updates via App Store.
Update Server.app. (Via App Store.)
Open Server.app and ensure that file service is turned on. It was turned off in my case so I just turned it back on after double checked the file and sharepoints and their permissions.
Test with client computer with smb://myserveraddress in Finder.app via "Connect to Server" menu, this is so that you know it is working with SMB.


Out of the above, step 4 and 5 are the most important. In my case the latest version of Server.app was not compatible with older version of El Capitan (I didn't have the latest version of El Capitan as I didn't upgrade it from Yosemite through the App Store). So after upgrading to El Capitan, always install all updates available for El Capitan before proceeding to anything else.