On closer look at mission CWW-09-2, the 50% fuel load only happens when viewing the loadout in the mission editor. If you play the mission directly or play it through the mission editor without touching anything, the briefing will say the fuel load is 4355 kg (higher than the internal fuel capacity of the jet and no external tanks are loaded) but then when loading into the mission the fuel load is 2835 kg. In that case, the mission plays just fine.
However, if you load the mission in the mission editor, select the player's jet, and view the loadout, the fuel load often initially shows as 100% but then drops to 50% when the loadout tab fully loads. Perhaps it is correcting for whatever causes the fuel load in the briefing to be listed as 4355 kg, but in any case it's an odd behavior. Popping open the Lua file for the mission, the fuel field for the player's jet is indeed set to 4355.