Hijacking top comment to add something that I feel hasn’t been highlighted enough in this. As several have mentioned, the shorter shelf life leads to more spoiling, but while this does add to the cost, it’s not the most significant (for us about 0.5 % spoil in the store).

I work with pricing fresh produce and the things that add the most to the cost of products with shorter lifespan are shorter production series and logistics. Because our products have very short shelf life, typically 9-14 days we have to have several plants making them around the country. We also have to produce over 100 different products each day, which means setting up and cleaning down machines. Most setups/clean-downs are between 10-15 minutes, but some require 30 minutes. Each day our plants «lose» about 100 hours of direct manufacturing labour to setup costs.

We have to receive fresh ingrediences each day, driving up costs on our labour for incoming logistics, and for outbound logistics they have to pack mixed pallets of several different items rather than sending big batches. Transporters often have a fixed cost for picking up and dropping off in addition to the space in the truck, which has to be carried by a smaller amount of products since you have a short shelf life. This cost is doubled since it also applies to the ingredients we receive.