In 6.43 still I have now finally build a new super-fleet with, when united, a couple of 150mt fortress/city sector modules. It kind of proved anything wrong that I previously found out about the fleet fuel limitation. The rule about the number of error windows before was observed to be exactly one error per multiple of 2^31 as fleet fuel. I thought first that the ship count, mainly through a lot of fighters, would increase the problem, but this was tested negative with 480 fighters, 6 30kt long range bombers, and 2 20kt long range scouts docked, and still no increase in errors. Now I notice that this might have been because the dock there was a PDC hangar.
Anyway, so now I have 1mt capacity ship-based hangar filled with 720 fighters, 9 LR bombers, and a couple scout, science and transport supports, and I again get a couple hundred error windows upon selection. This time there is even just one 150mt civil module in the fleet + a 3 mt tractored military one (which is the hangar). This means that the additional error windows don't come out of things like overflowing cargo or fuel harvest capacity, which I suspected before. It really seems to be only fuel related, and in the format '1 error per ship' now.