Even when hiding inside the shuttle we continue to overheat, the only time we start cooling down at night, is this a bug?
This is an intended feature! Heat is increased by the outside conditions, being on a dusty planet that is naturally hot, but machines also throw off heat so while you are huddling around your spaceship those machines are throwing off heat as well. The key is to keep cool and hydrated, this means at the beginning you're going to have to focus on water and food production. If your camel pack has water in it you will slowly cool down over time, if you find yourself in dire straights several quest rewards include cool water, this will provide a big boost to your heating problems. You can also sit in a chair while sifting to slow the heating and hunger process. I can't remember if the ship has one, or it is a retaliative easy craft.