The IGCC station hold many secrets not known by most of the crew, these areas might be highly classified research labs to simple utility shafts that have been forgotten since the station was deployed.
When you discover a secret area a bell will jingle and a Hint will be displayed on the left-hand side of your screen. Secret Areas often contain rare chests and loot, log books with story background or world information but can also be a Zone Portal to a hidden map or be occupied as a hide-out for a Wandering Merchant.
Challenge missions are not marked as such in-game, but they can be identified by a more cryptic structure and descriptions. These missions are most commonly found outside the safe zones as opposed to the regular missions.
While these missions are more difficult than the normal missions, they do provide better rewards and often help you unveil secret maps, unique monsters, secret character classes and unique loot.