If you always ship all items in each order together in the same parcel, make sure you configure each product to use the same Packaging Type, and with an absurdly high Capacity like 9999 that would never be reached.
If you've defined a range of different packaging types with varying empty Weight and/or Cost settings (in Seller Admin > Cart Shipping Settings), but you could normally include smaller items in the largest container required for the order -- i.e., you'd normally ship an order for all-small items in a smaller box, but small items could go along with a larger item in its larger box -- then use our Tubes packaging types (even if you won't literally ship in actual tubes), as those can consolidate items to fill unused capacity in the largest Tube(s) required for each order.
The trouble you're seeing is probably happening because USPS and UPS provide no way to query for multi-parcel shipments of varying weights, so our live rate-lookups have to divide the total weight of the order by the number of separate parcels in the order, obtain a rate for that averaged parcel by itself, then remultiply that rate by the total number of parcels in the order. This usually works out fine, but it can sometimes produce peculiar results in fringe cases, such as orders combining items of widely-varying weights shipped in separate parcels. If your products are configured with a shipping Capacity of 1 and/or using different Packaging Types, we're querying for rates under the assumption that each item is being shipped in a separate parcel, rather than all being shipped together as a single parcel, and the (averaged parcel) X (# of parcels) is resulting in a higher rate than the sum of rates for each item queried separately.