I believe this occurs due to how bombers are treated as "dead" when they use up their payloads - you'll see their icon go dim in the UI at the bottom of the screen when they're out of strike ordnance. In this case, either the fighter will get back to the ship and reload, or it'll be intercepted and destroyed, and the ship will have to make a new one.
But here's the kicker!
The moment the bomber launches its payload and is treated as "dead", the carrier starts building its replacement. I think that when a bomber returns empty and lands, it isn't technically being rearmed, it's just triggering a rapid speed-build of the craft under construction to replace it (which then is launched shortly after to give the illusion of a speedy rearming of the previous fighter).
Therefore, if a bomber is detained long enough (by the carrier moving away, the fighter being EMP'd, or otherwise kept out of reach of its carrier) that it's replacement is completed under normal time restraints before it can return to its carrier, you'll see the event you've encountered there: A new fighter is launched even though the previous one has yet to return.
A fun little glitch (if it is a glitch), though not a gamebreaking one fortunately, since you can't exploit it to have more active (ie. armed) bombers in a wing than normal at any one time.
