During the scene that occurs in front of Lemuria when the player first arrives, answering "no" to a number of the questions, the available yes-no responses Kraden will give will be different. One of these lines comes close to breaking the third wall.

In the second The Lost Age Debug Room, "Psynergy Test", a Kraden NPC stands two spaces to the right of a flame. If the player casts Blaze on the flame to shoot fire upon Kraden, he will generate a "!" icon, hop twice, yell "GAH!", move two spaces up and left, generate a "head bump of annoyance" icon, hop twice again, and yell "What are you doing???" Now if the player moves below the flame and casts blaze again, Kraden will exclaim "YARG!" and move back to his original position in exactly the same way, yelling "What are you doing???" again.

Within the code for the game is an image of Alex that is somewhat different to the image of Alex seen throughout the actual games. Its placement in the game's code suggests that Alex was possibly going to be a playable character sometime during development.

The continent of Gondowan bears a striking resemblance to Africa. The name itself might be a misspelling of Gondwanaland, a supercontinent that is believed to have contained Africa, South America, Antarctica, Australia, and the regions of India and the Arabic Peninsula.

One of the game's dungeons, Air's Rock, is based on the real life Ayers Rock in Australia. Just as Ayers Rock lies in the Australian Outback, Air's Rock is found in the middle of a barren area. Its alignment with the element of wind could be a reference to the high winds that occasionally blow around Ayers Rock.

Inside the game's files are unused sprites of a character that resembles Link from The Legend of Zelda.

Before entering Lemuria, the guard at the gate asks if you will behave while inside. If you say 'no', the normally calm Kraden will snap and berate you for your incorrect answer.

After defeating the final boss of the game, the villagers in the town of Prox can have their minds read. They have special dialogue related to the defeat of the final boss or to the release of alchemy. This is impossible to do without hacking however, as neither Ivan nor Sheba are available at this point in the game.