Phantom Files, also known as Hidden Game Files, are files that are purposely hidden or improperly titled by Rockstar Games, intended to disguise and hide myths from those viewing on their PC.
There are thousands of files per GTA game, making it difficult for a single person to open and view every one. Most people just skim over and glance at the file names, looking for one to stand out. In most cases the person comes up empty, as they didn't find a file titled with the name of a specific item.
Because of this, it has become believed by some myth hunters that Rockstar anticipates that people are going to search the game files, so in an effort to keep a myth secret, they disguise the name as something that it is not; possibly placing the file in a category where it wouldn't belong in, like a model being placed in the audio section. Others argue that Rockstar can hide files from view entirely, making the file impossible to find.
Despite the claims of phantom files, their existence is highly unlikely. It is impossible for the game to turn one file type into another, such as an audio file into a texture file, without using some type of converter. Additionally, there is no reason why the game would install a file into a separate directory than what the installer chose, as it would be seen as an unethical move on the developers part. Also, it is not even possible for a game developer to hide a file from everything except a single program, including the user.
The only way for the player to experience a "phantom file" is to modify the game themselves, and then incorrectly uninstall the file. In certain circumstances, this can lead to the game searching for the nonexistent file that the player no longer be able to see, usually resulting in a crash or a glitched model in it's place.