Doing a binary search through my modpack I isolated the issue to this mod.
Sticks, cobblestone, really any item will at random times have stacks that refuse to merge. Usually it happens when you have a given stack or single item in your hand and try to get more of it through a storage drawer or harvesting.

There doesn't appear to be any NBT data that is different on either stack, and it can somewhat be mitigated by somehow in-game modifying (placeable sticks when broken will merge again) or dropping the items in-world to have them merge naturally on the ground if they complete up to a stack (you drop two stacks that are up to 64 and they will merge).

Details:
Forge - 40.1.25
Minecraft - 1.18.2
Materialis - 2.6.0

That was a pretty silly mistake with some pretty big consequences, fixed in version 2.6.1
For the record, this happens when you punch a block, which explains why it was happening with storage drawers.

That might be because it's breaking the crop and instantly replanting it, I'm not sure about that though.

It was happening with harvested crops as well, not sure if that's the same thing. Not punching to harvest, the quark right click to harvest.