Its not supposed to happen, if it does then its a bug, report it and move on. Bugs happen, nothing to get salty over.

As for the gathering skills, there are uses for deep vigor. I used it almost daily for HQ gathering and GC turn ins while leveling up; I still use it occasionally for some things. I much preferred that method over RNG because my luck sucks and it seemed to be faster than the other skills. You may not like it and chose not to use it but that doesn't make it useless.

I've also never had a problem with my GP once I reached 600 GP. I hit a node as soon as it spawn, fly to the next one and wait for my GP to recover, hit that one shortly before it times out, chug a cordial and repeat the process. Its actually a waste of GP for me because of how much the cordial gives but unless I mess up, I'm able to hit a node every 2 hours. I'm not sure where your problem is but it is definitely possible to hit each node. Maybe practice your timing? Use your skills faster?