Build fighters mission does not automatically load the materials to build the fighters. To do that, you need to use the "LFM" friendly code. Alternatively, you can load the materials yourself (3 tritanium, 2 molybdenum, 5 megacredits per fighter). You can use the +Fighter button at the bottom of the transfer screen to load things in the correct ratios quickly.
No matter which method you use, your main ship screen should display the expected number of fighters to be built if everything is set correctly, so that's a good way to verify. |