Yes, you could get screwed because both segments must have availability in order for either to clear (in advance). In the future you should use the multi-city function and book each segment separately... or have your travel agent do it for you.

This is a huge complaint and it comes up frequently on this board. They also screw you on the mileage earned when there is a "direct" flight with a stop.. you will earn miles based on the nonstop distance, not your actual flown miles. Not a major difference in this example..but on other routes it can be more significant.