Remember, units that you build with a base that cannot be stored in the cargo of the base will go to any other cargo space present in the sector, i.e. other cargo ships or planetary cargo. What I like to do is to build a cheap base with only a space yard on top of a planet and let it build weapon platforms. These will be dropped right to the planetary cargo when completed, you can use emergency build with your base (it's a "use only once" base
) and it will keep the more productive build queue of the planet free to build facilities or ships.