After "some" work, missiles actually fly, and home in to their targets. It turned out to be much harder than I thought they'd be. Most problems came from improper math calculations. Especially hard to track were bugs that were related to local coordinate system of the objects, which caused problems for missile rotations, spin, and control thrust. This in turn caused confusion in the controllers that did not receive correct missile status, and made wrong decision how to correct them.
What this means for bug fixing, is that there were multiple layers of interactions, so a digging was necessary to identify actual problems and not their results.
Man, I imagine how much work it took to implement control for real-life air missiles.
Here are missile trying to hit each other. Yeah, missiles at the moment are trying to hit anything you click on.