Trolleys
Perhaps because this place used to be a train station, there are trolleys in the Akihabara Layer that allow you to explore distant rooms and areas. They can also be used as shortcuts.
Levers
You can use the levers to switch the direction of the trolleys. Use them to get further into the layer.
Magma Floors
There are magma floors in the Minakamiyama Layer. You will take damage if you walk over them, so be careful.
Pits
There are many pits that will drop you down to the floor below. Sometimes you may find surprise treasure chests.
Containers
There are puzzles that involve moving containers in order to open paths, or returning misplaced containers to their proper place in order to open doors.
Valves
There are sections in the Umeda Layer that are underwater. The key is to use the various valves to fill and drain the water.
Phantom Walls
At first glance, they look like ordinary walls. But when you touch them, you'll find out that they are just an illusion. If something seems fishy, try walking through the wall.
Solve Puzzles to Find New Paths!
As you continue further into the game, more riddles will come your way and the difficulty will increase. Each floor has hints. Use them when you're in trouble.