Let's start with just basic things, in-universe of course.

- The Child could be a Psyker, making every warp trip dangerous and spooky things happen frequently.
- The Father could be a powerful figure in the sector/Imperial Guard, bringing unwanted heat onto the group.
- The Child has had it's life ripped away and their mother killed all in a very short timescale, hello mental issues and freakouts!
- The Boy has to grow up. Make them RP the talk. If you do, please please make a record of it and share it here.

Other than that I agree with Laughingmanlol. Do not let the child become a background image. Don't make them a JarJar level of annoying, but just make them a kid on a spaceship who has had a pretty bad hand dealt to them. Nightmares would be my first thought. Every night. For months.