After purchasing a Bundle or Ancient Coins through the Sea of Thieves Store within Steam, your purchases are initially added to your Steam Inventory. To then apply these purchases to your profile you simply need to boot Sea of Thieves where they will be 'consumed'. After this, all contents will be made available in-game and also the purchase will then be removed from your inventory.
Sometimes though, when purchasing a Bundle you may see the message highlighted below:
This is due to already having purchased a Store Bundle that is already within your inventory (which has not yet been 'consumed') and is designed to prevent multiple purchases of the same Store Bundles at the same time.
Please note: this will not generate when purchasing Ancient Coins.
In the event that you do accidentally purchase the same Bundle more than once, please contact Steam Support for a refund: https://help.steampowered.com/