Overlapping planets seems to be an accepted 'feature', but I see no benefit and it just makes it harder to perform actions in the correct gravity well. Unless the two planets were given a single gravity well, I would think it better to get rid of overlap due to the gui problems. I understand it has some novelty effect, but otherwise is there any reason not to remove these?
Report it as a bug? Maybe they need enough pressure. I've really had faulty behaviour due to overlapping gravity wells.
It's one of the things (missing multicore support is worst, though) why I decided to return the game to the store until there's a patch for sins (I'll rebuy happily) or they deliver a better Sins2.
Screet