On a fresh install of Skype for Business, I created one and only one dial-in number but this one wear appearing twice when creating a “New Skype meeting” from Outlook.
We discover that this was the case only when using Outlook 2010 or 2013 with the Skype for Business client 2016.
This was not the case when using Outlook 2016 or OWA.
The only workaround I found was to create a second dial-in number for a different language (One for English and one for French) then both numbers were appearing and no duplicates.
FYI, I was running Skype for Business Server 2015 with CU4.
Hope it will save you time troubleshooting.