If you have bought the game and not received the discount please contact Valve. here:
https://help.steampowered.com/en/wizard/HelpCompletePackagePurchase?appid=1016790
This discount (as long as you played the open beta) is guaranteed - so please know that it will be honoured.
We are in contact with Valve right now to get this issue rectified and it will be sorted as soon as possible. This discount is applied in the Valve end of things so there is little we can do from a dev side, but please know, the discount will be honoured and we are doing all we can.
We apologise for the inconvenience.
UPDATE
The issue has been fixed.
If you purchased the game and you have less than 2 hours gameplay, please request a refund and then purchase again - the discount will show up now! You can do that here: https://help.steampowered.com/en/wizard/HelpWithPurchase
And if you have more than 2 hours gameplay - create a support ticket here and Steam support will sort it out for you. They are ready and willing to sort this out.
https://help.steampowered.com/en/wizard/HelpCompletePackagePurchase?appid=1016790
Also, as some people have been asking - yes the discount will apply to the bundle as well :)