Seems people have been having trouble accessing their extra content such as the ghost skins and vanguard armoury with complaints rising on the bungie support forum.
As i'm on the ps4, I managed to fix the issue by restoring my licenses. To do so, go to Settings -> PSN -> Restore Licenses and then the pre order bonuses should be available when you relaunch the game. Seems to be an issue with digital downloads as far as I can tell as the extra items weren't downloaded properly when preloading.
EDIT: I'll try update this with additional methods that people used to get their bonus content working.
Turned off the PS4 and turned it back on first, restored licenses again and under Destiny, in "Related Items" the DLC finally showed up. Credit: seooo13
Turn your ps4 all the way off (not stand by), turn in back on do not start destiny up, renew licenses, turn it all the way off and on again. This is the only way it worked for me. Credit: T1cklish
Log into the web store and download the expansion pack then download the vanguard armory. Then it was there after restoring licenses. Credit: mastamind229