I found https://connect.microsoft.com/SQLServer/feedback/details/797967/ssms-create-script-duplicates-the-statements-for-grant-or-deny-column-permissions and the response from Microsoft is that this has been fixed. I have not made research to see if the fix is included in any of the most recent cumulative updates to SQL 2012.

Note that if you install the update, it's important that you apply on the machine where you run SSMS, because this is a bug in SSMS, not the engine itself.