Had some problems with my system yesterday. I built the requisite number of Halley's and engaged an asteroid to destroy a planet, but it never left it's own planet's orbit (even after "two years" [orbits of sun]). The system was built as follows: Planet A, orbits Sun asteroid 1, [near] orbits planet A asteroid 2, [far] orbits planet A Planet B, orbits Sun Planet C, orbits Planet B asteroid 3, [near] orbits Planet C asteroid 4, [far] orbits Planet C I build the Halley's on asteroid 3 and engaged them to destroy Planet A. The asteroid never left or altered orbit of Planet C. Also of note: Planet A and Planet B were designed, built, simulated, and saved to have large elliptical orbits of the Sun in the system manager, but in the game they played as though they had circular orbits of the sun. (which made for occasional moons passing through planets undamaged) I've only been able to attempt this planet smashing once, so I'll update as time permits.
It's possible that assigning them elliptical orbits broke their ability to be used as planet smashers. The system isn't very robust at the moment. I've had no problem smashing asteroids into planets for "normal" systems, which is to say, systems designed to not push any limits: limited number of bodies in roomy, circular orbits.
There is bug where the planet smash sequence will fail if you don't zoom into a planet to select a target location. this bug has been fixed (but might not have been pushed yet).