Yes, you'll run across places where there are a lot of broken nodes, other places with barely any broken nodes.
Personally, I'm going with the theory that there's some way that a player can interact with the node that causes it to break (partial looting, full inventory, oddness with the companion's looting).
I've also wondered if somehow double-looting causes it - i.e. you click on it and your companion starts looting, you don't notice and do it yourself. I tend to do that by accident occasionally, as earlier in the beta looting it yourself was the default on right-click, and I've noticed a node that I harvested then came back around to was glitched the next time I saw it (less than 10 minutes later).