Star Trek Fleet Command is a strategy game and as such it offers the opportunity to further increase your strength in the game or focus on different aspects of your development by using Researches, Bonuses and Officers' abilities.
If your officers are giving you an additional hull bonus during battle, it may happen that you win a battle, yet your ship gets destroyed anyway. The reason for this is that the additional bonus hull granted by the officers would protect your ship up to the moment of victory; once the battle is over, the bonus is no longer applied and depending on your remaining health and hull stats, your ship may end up being destroyed. This is intended behavior and a little strategy trick you could use to boost your ship's stats. Note that your victory would count towards your missions as usual.