What device are you using, and what OS are you running? I'd like to make sure I can replicate the issues. I am aware of a factory having nothing in it being a bug.
On a side note to build something you click on the build icon either on the planet when looking at the system view, or the build icon on the Planet Detail screen. Looks kind of like a little factory. You don't have to click on the factories. When you build something an open factory will be selected.