The Ink Bottle can be found underneath a drawing board on the left side in a room full of desks, past where you first started Bendy and the Ink Machine.
Where can you find the Ink Bottle?
This is a bit of a walk because you’ll need to go past where you first started the game.
Exit the pedestal room, hang a left, and take the left down the short hallway. Turn right and keep going straight through the main open area (past the Exit sign) of the place you started until you hang a right into the drawing board room. At the far left corner there’s a desk with the Ink Bottle at the bottom.
To return to the pedestal room, follow the main hall out into the open, and make a right where you see the sign board for a variety of locations. In the long corridor, take a left at the short hall, a right, and then a right to the room at the end.
The Ink Bottle belongs on the far left pedestal.