I've only seen this once, but at one point I was unable to create a fleet of 3 units, despite having ample logistics to do it. Each time it would create one fleet of 2 units and leave the other one out of it. Pressing create fleet with the 2 units and other one did not help. I think this probably has something to do with the fact that they were both different version of the same named ships. Then again, maybe not.