Situation:
I had an existing cap ship factory. I queued up 10 or so cap ships by selecting the planet and queuing them up from there (i.e., not queued at the cap ship factory itself). Then I queued up 2 more cap ship factories so that the ships could build in parallel.

Problem:
After the second and third factories were completed, ships were being built in parallel but they were all coming out of the same cap ship factory (the original one). They were coming out 2 or 3 at a time but at the same factory. They probably should be coming out of the factory that actually built them.