In the Hall Of Heroes, go to the graveyard and find the three graves in the northeast part of the field with the following epitaphs, all of which reference game features that did not make it into the final version:
If you finally have access to Antonia South, go to another gate and leave from there. Once in the temple where the seer is located, he will teach you "Cash Drop", but it will say "Freeze". After you go back, the gate is open and remains that way but you cannot learn "Cash Drop" anymore, even if you have completed the game.
Meet ranked Clockworks that are coming in Battle mode by doing seige. However, if you do the northern gate siege, you will see green Clockworks. Copmlete the Boss "Beast" to get 10,000 source. This siege tower isn't in the story.
Complete the game, then hold R and select your profile to replace all clockworks with Kingdom Force and see Bluebits instead of Sprites from Clockworks during the intermission sequences. Hold L and select your profile to view the ending sequence. Additionally, load your cleared saved game file. Go to Brookwood Camp, and use a skull on top of a grave to display a yellow dot in the world map. There will be no other dots leading to it. Go to that location to find a cave. Pop the bubble in the water. Activate the source well. All the lamps except for one will light up. Use the unlit lamp to reveal a door which opens to the developer's room.