What you're describing sounds consistent with an expected checkout behaviour, which combines shipping rates from different shipping profiles (described in more detail here: Combined rates at checkout - Help doc).
If you decide to create multiple shipping profiles . . . then some orders might contain products from different profiles. When this happens, the separate shipping rates for each product are added together. This provides the customer with a single shipping rate at checkout.
By this rule, when a customer adds a product from profile A (which offers free shipping) and profile B (which offers $5 shipping, for example) to their cart, the total shipping cost they'll be asked to pay is $5.
What I'd recommend, since you're looking to avoid this behaviour, is you explore a couple of these apps available in our App Store, to create your own custom shipping rules:
Both apps offer a free trial period, so definitely take the time to see which one might be better suited for you.
I hope you find exactly what you're looking for!
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