What is happening is that the node has been recently harvested. It still shows in game but as unclickable. From a distance you can hover over the node and if the "harvest" arrows show up then it is harvest able again.
Or you can sit and wait for it to reset.
This is simply not the case.
These nodes are still exists, some are hidden in obstacle of the map, most simply cannot be harvested.
This is already something being patched in 1.0.1 per the patch notes.