Bungie just put out a tweet that they're investigating an issue where Shadowkeep purchases aren't being properly granted the Season Pass. The Upgrade edition gives you the SP because Shadowkeep is part of the bundled purchase, so this is affecting you as well.
https://twitter.com/bungiehelp/status/1311761133473157120
Unfortunately, until the issue is resolved, there's not much you can do outside of purchasing it directly yourself. I'd suggest waiting if you're able to do so just in case it gets fixed soon.
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Thanks, hopefully its sorted soon.