I have a feeling it is rounding off the numbers somewhere. So that your logistics total is actually something.g like 41.4 and so it is not allowing the fleets to combine.

The ship designer does this with component sizes. It shows an even number in one place, but in the details you see it has a decimal value that exceeds the value shown. So if have five spaces left, you select a component with a value of five but it won't let you add it. Then you look in the details and it's like a 5.3, which exceeds the remaining space you had available. 

Just guessing it's the same kind of issue. Since so many bonuses are percentages it would affect almost all the values in the game. Unfortunately, the game is notorious for hiding this critical information from the player.