Keep watching, they should separate. When they go to the same star system, they should explore different parts of it to speed up the system exploration. If that's not happening, let us know.
In 22.214.171.124 at least, that's how they behaved. After building two at the same spaceport, they both went to the same planet to start with, but after that, they separated and each scanned a different part of the system, then they moved on and scanned the next system together. At the end, when all systems had been scanned, they were all clustered together around one point in the clouds. :)