There are problems with designing upgrades to the pre-designed ships in the game. As an example, lets look at Colony Ship:
1) Go to the design screen and select Colony Ship
2) Click Upgrade
3) Add two Sensor components to the colony ship
4) Select one of the Sensor components from the list on the right-side on the screen. Click the Remove button.
5) The "space left" meter changes from xx/65 to 0/0
- Proud Canadian