Chapter 1: Whisper = In the glass walkway before the maze, the dots are on the back wall of the left flank.

Chapter 5: Puzzle = The dots are on the wall right after completing the puzzle.

Chapter 7: Down = After exiting the prison building, the dots are in the outside plaza against concrete arches and gravel.

Chapter 8: Notes = In the ramps leading down to the puzzle with whispers, the dots appear on the inward cliffside close to its entry way.

Chapter 9: Escape = In the third version of the prison room, the dots sit plainly on the left wall.

Chapter 13: Mobius = In the ship's center control pit, the dots are on the right wall as you enter it from the front.

Chapter 14: Island = After entering the two-way island and progressing the dialog for the next island to appear, the dots can be seen on the left side of the new island from the old island.

Chapter 15: Machine = The closest thing we have is the machine's gear configuration. It's not entirely clear if these are the same three dots, as the design looks significantly different here.

Chapter 16: Tower = After the impossible door is opened, walk along the path until the invisible maze area is seen fully from above. Below will be three spotlights showing the dots' pattern.



Chapters for which the three dots have not been spotted (yet):
Intro
Chapter 2: Backwards
Chapter 3: Entering
Chapter 4: Stairs
Chapter 6: Exiting
Chapter 10: House
Chapter 11: Lecture
Chapter 12: Theater
Epilogue

If anyone can find the three dots in these unknown places, please let me know so I can update this video in the future.