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I believe Carbonite can't register a node until you've fully harvested it.
Of course, I can't be certain about how Carbonite adds nodes, but I would imagine the actual node-creating process starts with casting the "spell" that harvests the mining or herbalism node, and ends with the looting of the contents.
For example, say I run into a Wild Steelbloom node, and I can't harvest it yet. The harvest "spell" doesn't work, Carbonite doesn't trigger... and even if it would, it'd have no clue what kind of node to put down.
I return fifteen minutes later with a high enough skill, and the "spell" works as it should. I recieve loot: [Wild Steelbloom]x2, which Carbonite registers and puts a node where I'm standing.
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