I think that's a bug, if that's what's really happening.

You can discover another civ by moving your ship next to it's area of influence - that is, be in a space right next to one which they have influence over.

Being a couple of spaces away and merely being able to see the other civ's planet doesn't count as "contact".

I have got thousands of hours in on the game and haven't seen that behavior.  You gotta meet someone, flight crew or planetary staff, to make contact, but then it happens right away.  If it happens again, document what you can and submit a ticket to Stardock.  They'll need a clue to find it if it is as subtle as it could be with such strangeness involved.

The minor world has to be within sensor range of one of your positions.  They're not in the UP so you can't use the Diplomacy screen.