I found out what happened, kind of.
The dealership sent a check over to toyota financial, and instead of paying off the old lease, they incorrectly applied it to the new loan. Or at least they tell me that is what happened and they are trying to straighten it out.
What I don't understand is wtf account did they pay off? They claim it was the lease, but that is not how leases work. When my wife leased the car they take a down payment, then you owe X dollars spread out over the life of the lease. So she had 36 payments of $X (i don't know what it was exactly). On the last month she had the car she made the final payment on the lease and her balance was $0 because she didn't owe anything on the lease anymore. So how the fuck does her lease account have a $10,000 balance at the end of the lease when her balance was at $0? How can it simultaneously be $0 and $10,000? I thought maybe there was some third account between the dealership and toyota financial that they use for accounting purposes, but the loan that got paid off was not a third loan, it had the same account number as her lease.
The whole thing doesn't make any sense to me.