So, I booked a flight on the phone from Houston to Anguilla. It departs Houston, arrives in Puerto Rico, then you get on a small plane (I think Cape Air?) and take that to Anguilla. Then, same on the way home.

Well, I got my official itinerary email today and the only thing it says is the flight from Houston to Puerto Rico... then from Puerto Rico back to Houston a week later. The connecting flights aren't there. How do I make sure I have a ticket on that connecting flight? Blaaaaah this process has been a PAIN in the A

First one is the itinerary where it just says houston to puerto rico with no mention of Anguilla...
Second screenshot is all the flights that should be there. It won't give me the seats on the connecting flight to Anguilla, but at least it acknowledges the flight... Notice how it says Houston to Puerto Rico..... Puerto Rico to Anguilla..... then on the way home it's Anguilla to Puerto Rico then Puerto Rico to Houston.