There are three Secret Chests that require specific actions for them to appear and become accessible. Without performing those actions, these Chests even though may be shown on map will not be physically available.
- The Crossroads, main Plaza - 500 Currency Souls - break all six fire hydrants
- Choking Grounds, graveyard - Lifestone Shard - destroy all the big grave stones
- Twilight Cathedral, basement - Bloodthirst - light all the torches
It appears that in Darksiders 2, chests are automatically marked on the map.