Me and my friends who are all over the world have been testing this and for what its worth (until its fixed) here are a few things we noted about what works and what doesn't.
1. We have more problems in busier (highly populated) systems, though we play on private servers the population is made up of NPC's but this seems to still be the case. We have had considerably fewer problems finding each other after we went to less busy systems.
2. The determination of where you end up is made on start up not on log in. Another words, after you have created your group and everyone has accepted, have everyone shut the game down, have one player start up and join the private server than have everyone else start up and join the private server. This fixes the issue about 95% of the time.
3. Play on open server. For whatever reason, we have fewer problems on open servers than we do on private ones. 95% of the time we end up in the same instance when playing on open servers by default.
Right now though the multiplayer experience is quite terrible and clearly Frontier has noted that and are addressing it in an upcoming update. Strictly speaking though the game right now is suffering from quite a number of pretty gaping oversights, most of which can easily be fixed and have already been brought to Frontiers attention loud and clear. I think six months from now this game will be 1000% better if these oversights are addressed, the obvious one like you just mentioned is on the list as are a large majority of other silly things. It can be a bit frustrating though, I find the whole "everything in space is stolen" mechanic to be quite stupid. After all whats the point of being an explorer when once you actually find something if you take it, your a thief. Silly things like that I think will be addressed, hopefully sooner rather than later.
). Also, since comms are wonky at the moment, recommend using a third party chat program until it is fixed. eg: Mumble or Teamspeak.
