I've got the same problem (1.02.41), and the AI can do it too. The Arcaens took a few systems from me, and when I went to retrieve them, one of them had a full orbit of constructors, WITH 260+ CONSTRUCTORS SITTING OUTSIDE THE SYSTEM. I started to take them out, but with that many ships on screen each turn took forever (game almost seemed to lock up it slowed down so much) and they put new ones out almost as fast as I could destroy them. (Another nearby system of theirs had 100+ constructors sitting outside the system.) My distant and only remaining system was churning out constructors every turn as well, and I had military spending set to 0. I couldn't change the ship that was being built either manually or with the governor. I somehow was able to pick "Nothing" for my military queue (wish I could remember how), but then I couldn't build ANY military in that system from that point on. And, since that was my ONLY system, the game was pretty much ruined.
Of course, all this was happening at the same time that I had taxes set to 100% with govt. spending set to 100% and an approval rate of 100%. I somehow doubt it's supposed to work this way.