Perhaps in those missions, they had to bring in reserve craft and pilots? In the case of 'Love the Treason...', in order to provide extra protection for the Sunder, and in the case of 'Mystery of the Trinity', in order to search as wide an area as possible?
It seems sensible to have another 12 (or however many it's supposed to be) pilots and craft kept in reserve, and maybe operate them in rotation.
On another note, some squadrons fly more than one fighter or bomber class, so those units would probably be bigger than other squadrons that only fly a single class in terms of numbers of craft. I don't know if they'd have enough pilots to field both classes all at once though. FS doesn't provide many details to go on.
what FS calls wings is a "flight")
Yeah, they use that most of the time. I recall that in 'Mystery of the Trinity', Command says "All flights report in" at one point, but for the rest of game "wings" is used.