While not understanding all of the details of what went on, one thing is clear, one had better play close attention to the terms before making a substantial investment in a vacation package. I rarely purchase travel packages because they usually have rather draconian cancellation and change policies and I can usually find better deals on my own anyway.
Another tip is: When you have separate air travel reservations from a package, schedule some open time at your destination (e.g., a couple of nights in the starting city of your package deal with only changeable lodging reservations) before you begin your package deal. Personally, I would never take a chance on flying in just before starting a cruise or other expensive package tour that has very little time flexibility - although I know lots of people do this.