Is the son considered to be wronging his father for refusing to withdraw an amount from his deposit to pay off his father's debt, knowing that the father owns other properties and obstructed the sale of the agreed-upon apartment because of his refusal of the son's marriage?

If your father bought your share in the apartment and paid a portion of the price, with a remaining part as a debt upon him, and you accepted that, then the apartment has become entirely his. You are not obligated to revoke the sale. However, cancellation (i.e., mutual rescission of the sale) is more preferable and better, especially if your father is the one requesting it, because the Prophet, peace and blessings be upon him, said: "Whoever rescinds a sale with a Muslim, Allah will forgive his stumbles." If you are able to financially assist your father without harm to yourself, then promptly do so, for there is blessing and provision in it. Try to convince your parents of the necessity of your marriage if you need it to protect your chastity, and you are not obligated to obey them if they forbid it, provided they do not give permission.