If you look at the small print in holiday brochures it usually says that the final quote they give you is the guaranteed price you'll pay. But, in addition, you'll probably find a rider to say that any later increase in charges by governments or other regulatory bodies may be passed on to you.
This covers increases in fuel duty, higher airport security charges, departure taxes, and all those other add-ons they dream up from time to time.
Check again with ebookers. If the increase is to the actual base fare, I rather think that ebookers should be responsible for making good any error on their part.
But if the extra cost is down to the above taxes, etc, then I think it's Continental who may be within their rights to ask for more, (though it wouldn't be very customer-friendly of them).