Some Gathered ‘Wild’ Seeds do not stack with Farmed Seed - Kindling Shred is one, but there are a few - think Kranut also.
Some items belong to different smart stacks. For the examples you mentioned, Kindling Shred can be placed into an inorganic harvest smart stack:
Whereas Kranuts can only be placed into an organic harvest smart stack:
What OP means, is something i’ve experienced too.
Harvested shreds, won’t stack with gathered shreds.
This happened to me just after the update introducing the cement blocks. I had some gathered shreds. I then farmed some, dropped then into the same storage, but the 9 gathered would refuse to stack with the 7 harvested. No matter what i did.
I have since used up these shreds though 
So THAT was the issue I was having! I kept wondering why I had about 32 Kranut that refused to stack with any other Kranut I had.
Those 32 must have been Kranut I’ve gathered on an Exo trip…! I was SO confused about it, and actually got rid of them because of it. 
Thanks for going into further detail, I’ve added this to the bug database. So this is what I have:
Adding the middle items will work as expected:
But adding the item on the right creates a smart stack instead:
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Yep. That’s the exact same issue I’ve been having then, Dragon. I’m glad to hear it wasn’t just me losing it (more than normal 
).
I’ve got some Kranut that do the same thing, I’ve got no idea where I got them from though.