According to your screenshots, your Fletcher class ships have a Beam Fire Control, 3×Gauss Cannons, and a Commercial magazine with 100 capacity. Your mistake was in assuming that Gauss Cannons would need a magazine to store their ammo in, but that's not the case. Magazine components only store missiles, and you have no missile launchers. Luckily that's a minor mistake; just modify the design to take out the magazine and put in another Gauss Cannon or two.
If you did have missile launchers, then you would use the ordinance tab of the class design window to choose which missiles you wanted that class to load. Naturally, that would require that you had first designed some missiles using the missile design window.
