Weird routing for internal flights from Vegas

Just a quick question. My sister is on holiday after a bit of a messy divorce and has decided to go around california. She flew PE to LAS, stayed a few days there, then flew with UA to SFO, then today she flew to LAS with US but the flight was via LAS (taking four hours)
Not being really up on all booking methods (and to keep mother and father happy about their little girl) She booked the flights all through VS on the telephone (good price all in PE and internals for just under 900)
I can't understand why the agent didn't either book her on a flight that left ten minutes earlier direct to LAX from SFO? I did a dummy booking and the costs are the same. Also because of the one booking shes not been able to OLCI on any flights.
She has her PE baggage allowance but got wacked with $150 between LAS and SFO as she was four kilos over (despite pointing out she was on one big VS eticket) Is there any reason they would route her in such a way and does she have any comeback regarding the excess baggage charge as she was allowed up to 32 kg on the way out with VS who she bought all the tickets with?
Not being really up on all booking methods (and to keep mother and father happy about their little girl) She booked the flights all through VS on the telephone (good price all in PE and internals for just under 900)
I can't understand why the agent didn't either book her on a flight that left ten minutes earlier direct to LAX from SFO? I did a dummy booking and the costs are the same. Also because of the one booking shes not been able to OLCI on any flights.
She has her PE baggage allowance but got wacked with $150 between LAS and SFO as she was four kilos over (despite pointing out she was on one big VS eticket) Is there any reason they would route her in such a way and does she have any comeback regarding the excess baggage charge as she was allowed up to 32 kg on the way out with VS who she bought all the tickets with?