Left of the telescope area, at the area where you get the owl beside the temple, there is a tree. Spin it around to find a door that will lead to a small room. Once inside, you will find the stone that tells you what the tetromino symbols mean--when you move or press a button, the corresponding shape will light up. Hop down to the obelisk on the left side and perform the tetrominos on it. They are: UP, A/CROSS, R, L, A/CROSS, DOWN, L, R. When you do, the Anti-Cube will appear.
Once you've talked to all four owls, head to the cemetery and go down to the door that leads to the large owl statue. Once you arrive at it, the four owls will arrive and a secret door will open behind it. Hop through and then climb to the next owl statue's head to grab the Anti-Cube.
The 4 Owls Locations at night are:
To the right of the waterfall, there is a stone obelisk and a tree. When night falls, the owl will fly in to land on the tree.
The second owl can be found in the forest on the tree to the right of the hut.
The third owl can be found in the temple area that is located to the left of the telescope area. When the night falls, it will land on the tree beside the temple.
The fourth owl can be found in the windmill area to the left of the green sky warp gate hub. When night falls, the owl will land on the tree to the right of the windmill.
At the bottom of the green warp area, there is a door that leads to a room with a tall cylinder structure with ladders that can be turned. Once at the top, there is a treasure chest high above. Use the treasure to locate where the invisible blocks are and hop your way up to grab the Anti-Cube out of the chest.
At night, behind the large waterfall, there will be a set of symbols that appear on a door. Enter: LEFT, L, LEFT, RIGHT, R, DOWN, UP, L to enter. Once inside, you can find a blue tuning fork looking object. Hop on top of it and you will feel the controller start to vibrate. The beats that the controller vibrates left and right is the code you need to get the Anti-cube in this room. It is: L, R, R, R, L, R, R, L.
When you are in the dark room with the light blue platforms, there will be a second door with red blocks that blink in and out. Follow them up and when you reach the very top, there will be another Anti-Cube there waiting for you.