When you create a discount code on Shopify, it automatically defaults to not being able to work for subscriptions.
If you want your Shopify discount code to work on subscriptions, you'll want to check your Discount code to make sure it's set up properly.
From Shopify Admin:
1) Click Discounts
2) Click on the Discount code you created
3) On Purchase Type, click Both, so the discount code applies to one-time purchases AND subscription products
PRO TIP: If you only have it selected on Subscriptions, it will only apply to subscription products.
Make sure to double check your Maximum discount uses. It defaults to limiting the free shipping discount to the first recurring payment.
OR you can apply the Shopify discount code to all future recurring payments and give them free shipping forever.
5) Review your Summary and if it looks good to you, click Save.