There seems to be quite a few seating issues. Just flew DEN-SAN today and overheard several other people complaining about seating assignments.

We had booked MKE-DEN-SAN a few months ago through YX, and since the second segment was with Frontier, couldn't pick seats on that flight. A few days before flying though, I checked the reservation online and it now allowed me to pick seats. This was great since I was flying with my wife and 1 year old. So I picked the seats together, and when we arrived at the airport today the agent handed me two boarding passes with middle seats in different rows. Even though I had a confirmation email that had my seat assignments, she couldn't change anything. Thankfully we were able to switch with someone and avoid a tough flight.

So beware, if you booked through YX and have a segment with Frontier, I'd call to see if you can confirm seats rather than rely on the online service.