Ah I see. Didn’t even think of that but makes complete sense. This isn’t so much an issue with your third party vendors. It’s a limitation of Shopify. Why it is choosing that particular shipping option when it’s multiple vendors is probably a coincidence (probably a combo of products that doesn’t fit under the other option either due to price or weight) Can’t know for sure without playing around with it.
The problem you’ll have either way though, is that Shopify does not support multiple shipments w/ multiple carriers, on the front-end. The customer will be offered eligible rates on their order, and on the backend, depending on your packing materials, you may split it into two shipments, and you can, and you can also choose different carriers, but it’s not the customer’s choice, and if you’re dropshipping then you wouldn’t be the one doing that anyway. If you want to find an app that might add that functionality, I would search for the term “multi-vendor marketplace” probably.
Now, ignoring everything I just said, the fact that one rate is cross-border and the other is domestic makes me wonder if it actually has something to do with the product’s country of origin. Can’t be sure from here though without more info. Maybe modify them so both of them are under the same shipping zone, and then see if it’s still doing it. That will at least narrow the issue down to whether the zone, or the rate, is the problem.
To clarify, is this drop-shipping? Because in that case I’m not sure why you’d be the one dealing with the shipping rates anyway?