Yeah, I've been experiencing that for a while. I just thought it was in a kit somewhere. Actually, as I was writing this, I checked TIE's kit and saw the Unique "Eradicate the Weak", particularly the final sentence: "At the start of TIE Dagger's turn, recover 20% Protection per enemy with less than 100% Health". But then I realized it still doesn't make sense. If it happens early during the battle, there are only 3 enemies, the Dagger loses health, but no protection. If we go by the Unique, you would have to have 5 enemies with less than full health for the Dagger to recover full protection. So, either it's explained in a different ability/kit, or it's a bug.
Also, while we're on the subject of bugs, Fear. It's supposed to be just like the character version, you get inflicted with Fear, if you get hit before you take a turn, it's gone and your cooldowns are increased, otherwise it causes you to skip your turn. Instead, at least on enemy ships (I rarely have the enemy Leviathan reach it's Ultimate first, so I don't pay as much attention), most of the time, the ship gets inflicted with Fear, if I hit it, it's still able to use its specials, if I don't, the enemy just dispels it and takes a turn like nothing happened.