Yeah, there were a dozen or more pilots hanging around on board the ship the whole time they spent on Tatooine and Coruscant. Not just in this comic, but in the actual movie. What were they doing that whole time?

Transcript

GM: You fight your way into the hangar.
Obi-Wan: Are there any ships in here?
GM: Yes, the Naboo palace fighter squadron.
Qui-Gon: Great, we take them all.
GM: The controls are highly specialised. Only trained fighter pilots can fly them.
R2-D2: {aside} Pity none of you have fighter pilot software.
Qui-Gon: We'll sell them later.
Obi-Wan: Wait, what happened to all those pilots we rescued when we were last here?
GM: Err...
Obi-Wan: They've just been sitting in the ship since we left Naboo, haven't they?
Qui-Gon: They make a diversionary attack on the space HQ!
{beat}
{Pilots suddenly appear running through the hangar to their ships}
Ric Olié: There's our fighters.
Pilot 1: Finally! Some action!
Pilot 2: Three weeks stuck in that ship.
Pilot 3: I was going nuts.
Pilot 4: Damnit, I had three aces.
R2-D2: They get to fly into a suicide space battle??