Playing with a team mate this evening I discovered a couple of problems.....

1) You cannot enter the system together

2) It seems to scale as if there are 2 of you anyway

Earlier in the day I found that some of the missions require things like Medical Supplies or Provisions which are no longer found in the Replicator. These missions cannot be finished as once you go and get the supplies you cannot return to the system to need to help.

Hey, i can solve at least one of your problems. Usually to return to the system you were in, go to the cluster and find an unexplored system.

Now to the bottom right you should see a blue tab that says "Continue mission in System blahblahblah"
Click on it and...
Voila.

The top issue is something i agree with, exploration missions should take your team all together to the same instance.

The problems exploring in a team are here since early Open Beta, maybe even Close Beta. Report the bug again. As for the scaling, actually I think it's a feature : as long as you're in a team, the missions scale even if your partners aren't with you right now.