Slitherine

When a Colony ship with a Colonization module + Passenger Module
colonize a planet, i get the 1000 pop from the Colonization module, but the 5000 pop from the passenger module are lost !

Imagine yourself enjoying a great cruise on a passenger shuttle only to be dropped without any life support upon a lava.. err, let it be a desert planet.
Now, using your last bottle of water to get by you knock upon the colony module doors only to find that it's lifesupport machinery cant handle any more people and your only option is to wait for new dome to be built one year later. Water? No, sorry, we have a closed ecosystem - get out and die under the scorching sun.

tl;dr: you mass-murderer

The is a option in the game settings for do not lose the colonizer after the colonization.