It's caused by the change they made in 2.6 to the way reinforcements work. It used to be that the new ships would spawn and travel towards your fleet. Now they use the MIA mechanics that your fleets do when they get caught behind closed borders or your science ships does the experimental navigation, meaning they just vanish and reappear some time later near your fleet (except, of course, when it doesn't work and they just sit where they spawned).I wondered what was causing that!!! I keep having random one or two ship fleets floating around my empire and was super confused as to where they were all coming from.
I get why they did it. One of the most annoying things about reinforcement was that they completely ignored what was in their path. I would have cases where ships were getting picked off by enemy starbases that they blundered into. With the new mechanic, it's mostly fixed. Except, of course, when it doesn't work.