Just as the title says. It seems to me that when I was younger, fruit cocktail came out of the can all mixed up. Now it seems to be in layers. Peaches on top, then pears, then pineapple, grapes and cherries on the bottom.
Was it always this way and I just never noticed?
I’ve never bought a can that was layered. What brand are you talking about?
Del Monte No Sugar Added Fruit Cocktail.
I haven’t had fruit cocktail out of a can in years until I bought some for a friend staying with us. I thought maybe I just didn’t remember the layer thing, or maybe the fruit cocktail when I was younger had to ride on rougher roads on the way to the grocery store. 
I’ve noticed this, too. When I was a kid, it was mixed up better.
It may have something to do with USDA standards. Fruit cocktail is specifically defined:
30% to 50% diced peaches, any yellow variety
25% to 45% diced pears, any variety
6% to 16% diced pineapple, any variety
6% to 20% whole grapes, any seedless variety
little to no cherry halves, any light sweet or artificial red variety
In the old days, you’d just mix it all up and expect to hit the correct percentages. But they may have tightened things up, so Del Monte filled the cans one fruit at a time to avoid missing the legal percentages.
I wonder if that’s the order in which they are filled. If so, then the possibilities are that either they have come up with a less turbulent method (which allows the fruit to remain in the order in which it was deposited) or perhaps you just happened across a can that had been subjected to less fruit-combining turbulence.
Another thought is that something about the relative densities of the fruits results in the stratification, like jiggling a can of mixed nuts or a box of Crunchberries.
Ah, therein could lie the difference. The roads around here are shitty. I had to replace 3 broken axle on my last car - that I only owned 3.25 years - due to the poor road conditions in nearby Dover. All my groceries are probably quite well shaken.
If they were only being shaken (as on a rough road) and not flipped around, you’d actually expect them to separate into layers by size. Maybe not in the way the OP saw, though, unless those fruits are in size order.
I imagine it probably is a quality control concern as RealityChuck suggested. It may even be a slight benefit for consumers who really like most but not all of the fruits, although I don’t know how many people are like that.