Dire Nettle Spores not spawning

On my second play through I’m finding some of the spores are not spawning. Upon entering a new area in the zone there are plants that are empty of a spore. I didn’t experience that in my first play through, in fact I may have had an extra spore on my first play through. I have three growths that need to be removed.

Is this related to the boy at the blacksmith (I haven’t talked to him yet)?

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