I've noticed this in 1.6 as well as now in 1.7 beta 2, in fact I posted simular pictures. However, once again I was at war with another civ when through the diplomatic screen I had them agree to grant me a peace treaty while they gave me all thier planets, thus surrendering to me. They then turned over thier ships to multiple races.

After they weren't anymore, one of thier ships remained under thier control however, never moved. If I tried to attack it, it promted that I would declare war on thier civ. I have saved games of this after they were defeated with that one ship remaining. Why isn't this elimitating all thier ships?