As per the following post in this thread this is as it should be expected since upgrade processing was planned for the next patch:
Thx again for the info Apollo.
I think you both missed this little snippet of info:
In honor of this release, we’re making the 2944 Aurora LN available in the pledge store. Purchasing an Aurora package or addon will make the ship available in your Hangar after the next patch goes out Saturday. Upgrades will be processed in a future patch. Remember, all ships will be available in the finished game; purchases today are solely to help with the funding campaign.
There's nothing wrong. You will get your old aurora turned into the LN variant soon.