You can control the grouping of SKUs into submissions using the placeholders.
Probably you have chosen SKU specific placeholders. Therefore, a shipment will be created for each carton.
If you restrict yourself to general placeholders like "CURRENT_DATE" or "FBA_SEND_IN_NAME", the products should be automatically grouped into a single shipment.
You can also still set the placeholder / email settings individually for FBA Send-Ins or as a default for a warehouse: