If you have to pay more than you would to normally commute, they should compensate you for the travel expenses.

Personally when a company goes through the effort of organizing an interview (especially with travel) and I get there and some amount of chaos/disorganization is apparent I get extremely cautious and is a big red flag for me. Nothing like flying across the country (paid for) to arrive and have the person I'm interviewing with change and leave me waiting in the lobby 30 minutes.