Blatant robbery! Shameless bait and switch!
 

We purchased a around trip tickets with connections at EWR. On Nov. 9, 2009, we arrived at EWR. At the Continental airline International Transfer Counter near the international arrival at EWR airport terminal C, we asked the agent there whether we could cancel the 2nd segment of the flight (from EWR to BWI). The female agent helping us said yes. We specifically asked whether there would be any fees or surcharges. She said no. Then she asked whether we would also like to cancel the 1st segment of the return flight as well. After being confirmed it's free of charge, we decided to change the return flight as well. We were then let go without having to pay anything on Nov.9, 2009.
However, when we arrived at EWR on May 5, 2010 trying to check in for the return flight, we were forced to pay $220.38 for the difference of the two intineraries and $270 for the changing fees. With limited time left to take the flight, we had no choice but to pay the fees.
We have talked to the supervisors of the checkin counters, the customer service counters at terminals and the the floor monitor of the International Transfer Counters at the EWR airport but no one could explain why we were not charged at the moment of the itinerary changes while we had to pay afterwards wihtout being informed of any details of the fees. We were told to file a complaint on www.continental.com, which is the only way to contact them now rearging complaints. We did it right back at home. Nobody ever bothered to reply to us. Only after we complained to BBB did they response back, saying they didn't know why we were not asked to pay at the counter on Nov 9, but sorry, we robbed you and you have to suck it up.
I know these guys are in financial trouble now but bait and switch is not the answer!

You could have a chance of winning in a small claims court on this. As Continental specifically told you there would be no fees, and they seem to acknowledge this, you relied upon this assertion in making your decision whether to proceed with the amended contract. Continental accepted the amendment and you were now entitled to expect this contract to be honoured. I think you should consider filing in small claims court.

DO I need any proof?
 

Thanks for the info. The problem is I don't know what prI can show to the judge. Now Continental denied that they agreed to waive the charges in the first place, saying they could not find any record on it.

You have very good circumstantial proof that you were told there would be no charge. Had there been a charge, they would have levied it there and then. I strongly feel you have a reasonable chance of winning this.

Any agent can change reservations (flights, dates) without collecting payment. Many airport agents just keep quiet so they won't actually have to exchange the tickets (involving work). Then, when you go to check in for your new flight/date the system won't allow it until you pay.

That is deception, and they should be held accountable. I would love to hear the airline try to explain this in small claims court. The passenger was clearly lead to believe that this was being done at no charge.