These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Time passage is inconsistent. Every time you explore a planet surface, the counter is advanced by 1 turn, but timed tasks (ships en route, construction, research) do not advance. Order to build a factory, explore 100 sectors, return to colony — the construction would not advance. This also applies to Random Events with a time limit — e.g. when cryo-capsules on Calypso malfunction, you can start collecting ore and energy on the surface, and when you gather enough, there still will be plenty of time to build habitats.
Another useful quirk of time counter is that positions of planets depend on this counter, but ships move unpredictably when you spend turns exploring surface. If you don't alter the ship's course, it arrives to its destination when scheduled, but if you do, new time and fuel consumption are calculated from these incorrect coordinates. This allows to reach Beta asteroids and outer planets early in the game, before you upgrade the ships, without moving Calypso.
It's possible to give a task to a factory still under construction. When the factory is built, it finishes the task in a single turn. Useful for time-consuming shuttle building.
If you dismantle all buildings in a colony that has some humans, the humans will still remain there after you shuttle them to another place. This allows to ferry ("pipeline") unlimited number of people from such colony.
Mass driver was never intended for interplanetary hauling of cargo. Still some players managed to use it this way, despite the ridiculous resource cost.
Biota attacks on Gaia are triggered by building a second colony on Gaia, biota attacks on Rhea are triggered by building a colony on Rhea. You can colonize other planets, dying out won't be an issue as long as there's a single colony on Gaia. This allows to amass resources, do research and run some non-essential Apocalyptic Log investigations making you better prepared for the crisis. You'll still need to build those colonies to advance the plot and access some parts of Tech Tree.
Actually, there are several different triggers: building more than 3 colonies on Gaea + 2 on Rhea, or building more than N colonies elsewhere (I forget exactly), or enough time elapsing (hard to tell exactly due to the schisophrenic time count), and I'm still not sure if that's all.