Three dots

The three dots are a recurrent symbol in The Beginner's Guide. They first appear in Whisper (see gallery).

In-game, Davey Wreden never actually mentions the dots until the end, when recounting his various questions. According to his dialogue, Davey does not understand what the dots mean, and when asked, Coda wouldn't answer.

In another game by Davey Wreden, The Stanley Parable, there are three dots in an unreachable area in the warehouse.

When the dots are seen in Puzzle, right after the player is first introduced to the recurring door puzzle, Davey says that "we're going to see it a lot". Although he is directly talking about the door puzzle, it has been brought up that this may not be a coincidence and that the player should take this to mean that the dots will also be seen again "a lot" throughout Coda's games.

Interpretations
Since the three dots seem to be stamped on the machine in the Machine level (as cogs) - and that, in that level, the machine itself is Coda, the simplest explanation is that they are just Coda's "signature" as a game designer.

One interpretation from Steam user Snorlax Is H4x:"The game explores the idea of 2 doors and a 'dark space' in between. I believe the dots are the 2 doors and the middle one is the space between the doors, the place for reflection. This is also a metaphor for past, present, and future, the middle dot being the present."

Other Steam users mention how the dots resemble the icon for Steam itself, the world's largest game distribution platform, in which both The Stanley Parable and The Beginner's Guide were released. Although a far shot, this would resonate with the interpretation that Coda represents real-life Davey after the launch and success of The Stanley Parable (more details here). It also resonates with the idea of the Whisper Machine's "whispers" being all the feedback (conceptual or actual) generated after a game is released and then becomes not only owned by its author, but also by its audience, who is free to project their own meanings and interpretations into it and its author (which is also a main theme for the relationship between Davey and Coda in The Beginner's Guide). This process is known as the death of the author.

Interestingly, the mathematical sign for "because" is also three dots in a similar arrangement (∵).

Trivia

 * Weirdly enough, House's three dots do not seem to appear in the game, despite being on the map in Source.

Gallery
The three dots as shown in Coda’s games: