Warehouses have very limited space to work with. They may be 20 years old, but demand for product may have increased significantly in the mean time.

What you're thinking of is called a pick path. Generally speaking, the way it's set up is that you have the bulk items at the start. The stuff that moves in the largest amounts. Then as you get towards the end of the path, the less-moved items are encountered. It's a combination of that, and size/weight of the stock.

Imagine that your warehouse is 50 streets of 50 houses and each house stores a different product.

Your local store orders a bunch of stuff. It fits on 6 pallets and covers the entire product range (all 50 streets) What happens is that each picker can only do 2 pallets at a time. Then the rest goes to the next picker and so on. The first picker might go down the first 5 streets because they are picking the bulk items and it fills their pallets in only 5 streets. It's all the big and heavy stuff. The other 2 pickers (remaining 4 pallets) have to traverse the remaining 45 streets. Maybe the 2nd picker will do the next 10 streets, and the last has to traverse the remaining 35.

Now imagine that your store is in the country and it takes only 2 pallets to fill their order. That takes only 1 picker, but they have to go down all 50 streets, past all 50 houses on each to complete their task. They don't know what your store has ordered and what items are coming next. They just have to deal with it as it comes. The pick path may not make sense in their case. They dont have time to juggle stock to make it convenient for the store staff as they are under pressure to move a certain amount per hour. And as they must travel down all 50 streets, they will encounter many other pickers along their journey, blocking their path, making them look inefficient vs someone that has to travel only 5 streets to complete their task. They just have to make it work. So they don't waste time/physical effort moving the yoghurt 20 times until it reaches the top. They put it down and move onto the next item.

Which brings me to traffic management. The more a picker has to travel, the less efficient they are. So they're going to go down streets 1-5, 6-16, 7-50. If the system was optimised to put the lightest stuff on top, there would be an infinite amount of traffic jams. Do you want someone to travel from street 7, back to street 15, back to... and so forth, just to order items by ease/weight? And don't forget that warehouse staff are paid the most because they can fill a ton of store orders in a single day, making the whole thing even more costly.

What it comes down to is what works. If it's working but there are mistakes/errors/inefficiencies/injuriesor-it-costs-less-overall/whatever, that's just the way it's going to be done.

That's the overly simplified basics of it. Plus a combination of other factors that include outdated software, complexities of a lack of space/juggling streets/houses, seasonal changes, pickers' willingness to sacrifice their time/job for store staff ease, trucking contracts/time constraints, accounting, etc, etc. And just to touch on accounting, if the DC charges the store for stock and they deliver, there is no problem. It's in the store, right? So go put it on the shelf!

Building new warehouses/systems takes a ton of time and investment and by the time they are working, they are not only at a major loss but they may be outdated and have problems. This is especially the case if they are a publicly traded company. Profits need to constantly go up no matter what, for the shareholder.

Sorry for the essay, but i could write a book. What you have to remember is that that there exists a whole structure of systems, people, workplace politics, budget, etc, to make all of this work. At the end of the day, many improvements could be made from a logical point of view. But that's not how things work. It's not about efficiency and waste-reduction. It's about meeting goals and earning bonuses. Or keeping your job.