In attack of the hawkmen he bluffs to a French higher officer he's "flown several times" (which isn't as untrue as it sounds but that's not the point) in hopes of landing a nice position as a spy for the French army. He ends up doing reconnaissance work in the backseat of a plane but no flying on his own. So, I don't suppose we can say there's much of a plothole there. In fact, at that point he's still afraid to fly and Remy comments on it (silly immature Indy). Hope that answers your question.