I know a few people have had problems trying to get just the Taken King Digital-only pre order (the £40/$40 one for peeps who already have Destiny and both expansions). Just here to help out as I had the same problem and it wasn't clear how to fix. You need to make sure you have actually downloaded the add-ons for expansions 1 and 2. You're Destiny copy probably already sees you bought and redeemed them, but the PS Store needs to see these add-ons on your console, so just go onto your Destiny app on your home screen, go to related items and the add-ons should appear, along with the themes etc. I have a feeling this may just be affecting those of us who bought the expansion pass rather than both expansions separately. Let me know of this has been any help.
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Thank u for advice saved me from a right shit storm!!!