Leaves and flowers that are obtained by silk touch do not stack with those obtained by shears. This also applies to enderman drops, although I don't recall which class their drops are in (silk touch, I guess). You can set down the silk touch leaves and shear them to get them to stack, but that's not practical. It does not work to throw them all on the ground as it has in the past with other items which should stack but don't.
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silentwisperer
migrated
I've noticed this for a while now. If I accidentally break leaves with silk touch, I get rid of them because they won't stack with the ones I intentionally harvest with shears.
I've also had stacks of normally harvested mushrooms, and mined endstone not mixing with those same items broken with a silk touch tool.
migrated
Same issue experienced: leaves broken with shears are visually the same, but do not tend to stack with the same type of leaves mined using any Silk Touch tool (tested pickaxe and axe). This bug has been around longer than 1.8.1; I think since one of the Aquatic updates. Can't remember nor test since when exactly. Windows 10 Edition - 1.9.0.
migrated
I've had the same issue with purpur blocks for a very long time now. After the 1.9 update the 'silk touched' stack was renamed to the file name "com.minecraft.purpur" or something like that
[Mod] OcelotOnesie
I'm having this issue on Windows 10 as well. Version 1.9.0
[Mod] OcelotOnesie
Affects 1.10.0.
Kayla O.
I just noticed this on Windows 10 1.11.1, too.
silentwisperer
Affects all 1.11.x updates
[Mod] OcelotOnesie
Affects 1.12.0.
silentwisperer
Relates to/is the same issue as: MCPE-44649
migrated
Trading with Villagers will also not work with item which does not stack.
This can be seen in 1.9, with shearing leaves and breaking leaves with silk touch. You will get 2 different stacks, that will not combine no matter what you do. Simple grow any tree, and break half the leaves with shears, and half with silk touch on any tool.