If you overpay because of a travel agent's mistake, the travel agent must reimburse you for the difference between the amount you paid and the actual fare. You must consider the proper fare at the time you reserved and paid for your ticket, not when a subsequent fare change was made.
If a travel agent charges you less than the actual cost of your ticket, you are not entitled to travel for less than the established fare. The travel supplier may require you to pay the additional amount due before you travel. Whether you can recover the difference from your travel agent depends on the circumstances. If you knew the correct price, agreed to it, and the travel agent simply hit the wrong key on the computer, you are not entitled to any compensation from the travel agent. On the other hand, if you didn't know the correct price and made your decision based on what the agent told you, then you probably can recoup the difference if your reliance on the travel agent's statement was reasonable. If you were told that a $999 flight was $799, your reliance would probably be reasonable. If, however, you were told that a $999 flight was $9.99, you'd be out of luck.