Shipyard keep saying too many ship in orbit despite not hitting logistic limit yet.

Hey Kisa, what's the logistic of the ship you're trying to put there ? You got 32 logistic available on that station according to the tooltip.

There is a logistics limit and then there is a ship limit. I dont recall the numbers but its like 32ish ships you can have in orbit regardless of the logistics amount. Fleets have the same limitation you cannot have a fleet of 100 fighters.