Ive encountered this issue a few times already. I have a fleet of 2 or 3 ships and then another ship is sent to rendezvous with the fleet in order to join it. The logisitics is fine, so I know that isnt the issue, but for some reason when I select the two icons (one fleet one ship) and click create fleet it wont work.
I tried disbanding the fleet and creating a fleet from all the ships again, but once more that one single ship for some reason wouldnt create a fleet even if it was with just one other ship.
So I gave up and a few turns of battle ensued where both the mini fleet and the single ship fought separately. Then next turn, cause Im a stubborn fella, I tried to create the fleet again, lo and behold this time the hold out ship nicely merged. This seems to be a bug since I can see no reason why the ship wouldnt join the fleet right away (again logistics were fine, I checked several times)