Perhaps it crashed into the sea? It isn't always safe to launch aircraft when in the biggest waves. You can orientate the carrier to face along the waves, or otherwise move to shallower water.

Even if that's the case, I honestly reckon that part of the game needs a rethink. In real carrier operations in less-than-perfect weather, launches are timed so that the aircraft leaves the ship as the bow crests a swell. They don't just roll the dice and send the aircraft on its way hoping that everything works out. Granted, this is more clear-cut for carriers that launch with a catapult, where the shooter will get the OK from the pilot they're good to go, then will trigger the catapult as the carrier starts to pitch up.

Similarly, the carrier will always face into the wind to get as much free airspeed for the departing/arriving aircraft as possible. They don't follow the sea; almost by definition they run perpendicular to wind-driven waves.

Fine, so accidents happen, but the notion that aircraft can end up in the drink even in modest sea states is hugely frustrating. If this is a deliberate part of the game, then how about adding a hold state where a departing aircraft is set in place on deck and then sits there until someone on the bridge pushes a launch button? That way the player gets more control and is able to time a fairly short, consistent process rather than having to drive the carrier for a much longer period while the aircraft is put onto the life, raised to the deck, backed out and then launched at possibly the worst possible time.

At the very worst, this could be optional; with the mechanism disabled, a departing aircraft would behave like it currently does without waiting for the launch signal from the bridge.

There is a suggestion on the features list to allow you to choose when the craft takes off. This would help fix this issue, although as Dev says, you tend to have to turn the ship carefully so it doesn't happen, but that isn't always easy. https://geometa.co.uk/support/carriercommand/2282