Engine Room patterns. On ships with x.5 engines per MP, SA groups engines backwards, where the last engine room wouldn't have enough power to move the ship.
example: BC hull needs 2.5 I per MP. SA groups engines 3/2/3/2/3/2 when they should be 2/3/2/3/2/3 for a speed 6 BC.
Fighter munitions. IIRC, I mentioned this before, but the F5 screen will not display fighter ecm and eccm pods for the magazine loadout. Nor will their costs be reflected.