Why airfare from SFO via Denver to Costa Rica is 50% cheaper then same day Denver to Costa Rica flight?

Airfares are calculated by a very complex algorithm. A lot of times fares do not make sense. For instance it may cost the same amount to fly 74 miles as it would to fly cross country. I have previously booked a first cl ticket from Corpus Cristi to Newark via Houston that was cheaper than the cheapest economy Houston to Newark flight (yes, even the same exact flight). When I called to cancel my Corpus to Houston leg, I was told that they would have to charge me an additional $300 plus the $150 change fee. A lot of it has to do with different fees and fare differences ociated with departure and destination airports.