As mentioned in another post (Bug graveyard, Some Nodes in Graph are shown intersecting links that they aren't actually connected to ), I also have a problem with overlapping nodes and links. I CAN manually move them, but as I accumulate more and more notes, it is becoming harder and more exacerbating to do so. It would be great to have this fixed in a future update.
(NB. I understand it might not be avoidable, as @WhiteNoise mentioned in the linked post, but it doesn’t look like the other poster added a Feature request so I thought I would just in case.)