I know this is super old, but I recently ran into the same issue. And there is no actual answer here, just a bunch of things to try.
I have found the answer:
The Apply button is disabled if the current settings don't pass validation.
If you run
nm-connection-editor by itself, then select your VPN connection, you will see an error that explains what can't be saved.
Correct those issues and the Apply button will become enabled.
In my case, I found that I didn't have a user name in the Identity > Authentication > User name field. Once I added my user name, the Apply button instantly enabled.
Hope this helps.