Recovery of embarked craft under fire. Sure, there would be scatterjump strategies to spread fighter wings to the four winds, to reassemble when the heat is off. But during that time the carrier itself would be vulnerable.
This assumes we've built in naval carrier-like vulnerabilities into its starship analog. A through deck, a frigate... These mixed use platforms have a limited fightercraft complement but maximize either speed or screens. The carrier can be envisioned as the third path-- a huge complement of embarked craft as the first design criteria with everything else subservient to that. In such a scenario, the ship is dependent on those craft for survival if detached from its escorts, and must be able to process them in as fast a way as practicable.
