In the first step the system returns prices for a whole number of flights. Once the user selects the specific flights they want the requirements state "The system prices the itinerary" I assumed (and documented the assumption) that this means the system calculates the total cost of the trip based on the segments the user selected. That was my assumption but the point is
you should make assumptions where there are contradictions in the requirements and document those assumptions.
On the other issue there is no mention of different classes of tickets. The requirements indicate there is "one flat price per destination" so don't make your solution any more complicated than it needs to be.