All ships contain clues. Most clues look like blinking dots on the floor (usually a corpse) or on a piece of furniture. To investigate the clue, select a Deadnaut and click 'Investigate'.
Clues will typically provide you with Knowledge, but some can also reveal undiscovered rooms, unlock doors, or provide information about the threats you're facing. The higher the Deadnaut's Investigation skill, the more likely they are to reveal some special information.
Once a clue is investigated, it will disappear. So try and use your best investigator.
Intuition is a mysterious skill. It's not well understood, but intuitive Deadnauts can instantly reveal hidden enemies, sentinels and distant rooms.
Most importantly, they're more likely to reveal escape hatches. This can be the difference between life and death, so it's a good idea to have at least one intuitive Deadnaut in the squad.