Really sounds like the CSA you got was being deliberately difficult.

I've never heard of a retailer wanting a whole package returned if something is missing out of it (when multiple items ordered).

Where I work, we do a lot of online, and often with multi-item orders they can be split deliveries. Mistakes happen and sometimes people don't get something they've ordered. We NEVER ask for the whole box to be returned. (funny, though, when we send too many items, very rarely does the customer send us a note about that!). We'd take a photo as proof, and follow up with the place it was packed and sent, and in the meantime send out the missing items.