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The game (version 1.1) seems very picky about the conditions where it will spawn seeds from fae trees (the red-leaved trees that drop seeds which explode on the ground), at least with the tree in the middle of Shamazaar. I need to look up towards the top of the tree and move around while I do so, otherwise no seeds will appear. I do not think it behaved like this in the original version of the game. Provided this is not some quirk that only happens to me, I would hope this is something that is changed in an update.
a while ago i encountered a different bug with the seeds, which they then fixed. maybe what you're experiencing is a new bug that their fix brought..
you're not the only one with this problem fyi:
https://steamcommunity.com/app/336610/discussions/3/618459405721104927/
https://steamcommunity.com/app/336610/discussions/3/598198356167735219/

haven't seen a post of the developers in a while though, so i wouldn't get your hopes up for a fix.