I have seen the exact same thing in multiple versions. This time:
I had the graph view open in one pane when I updated to the 0.6.2 release. On starting up the new version, the graph view showed everything on top of each other in one small part of the pane! I closed that pane, opened a new pane and hit cmd-G but again it showed the same thing. But this cleared up on restarting Obsidian, where I had the expected graph view. I restarted obsidian again and I saw the same thing.
Some more detail:
I have two vertical panes, the right one split in 3 smaller panes and the left one in two panes. The graph view is in bottom left pane. When it gets in this mode, I close the pane, resplit the longer pane and hit cmd-G. Almost always now it shows the expected view but if I restart it goes back to the messed up view.
The common theme seems to be to close obsidian with a normal graph view in one pane. On restart it is messed up.