By default, both your products and your Brand's products count toward your free shipping threshold. This was designed with the best customer experience in mind. Brand shipping rates are still added separately for Brand products in the order.
If you do not want Catalog products to count toward your site's free shipping threshold, navigate to Settings > Selling preferences > Integration settings > select Separated for your Include towards free shipping setting.
The separated shipping option does not currently work with third-party originated shipping rates (e.g., Recharge, ASR).
Note: For this feature to work, you need to download and onboard onto the Catalog for Brands app. You are required to have both apps for Catalog to correctly calculate your cart's shipping totals. This is currently a beta feature.