It doesn't sound like it was Alaska's fault or Continental's. The blame lies with your travel agent. Even if the airline changed your ticket it was up to the travel agent to notify you of that change but that doesn't sound like the issue here. If the Alaska flight was indeed overbooked they would have notified you of that when you got to the airport and re-booked you on another Alaska flight if they had to involuntarily deny boarding. It sounds like the travel agent was trying to get you a lower fare which may or may not have been available. The "confirmation" you received from the travel agent may have listed the Alaska flight and the fare, but in fact there may have been only a request for space at that fare by the travel agent which was not truly confirmed. Most likely when Alaska notified the travel agent it was unable to confirm the seats at the requested fare the flight was probably overbooked at that point and your travel agent scrambled to get you on whatever was available at the lowest cost which was Continental.
My advice would be to contact your local BBB to register a complaint and check for other complaints against this travel agent/agency. Also if the agency is a member of ASTA (
American Society of Travel Agents) you can file a complaint with them.