The article didn't mention corruption but I would not rule it out. Follow the money. Whose pockets are being filled when one transit agency is paying 2x what another one does for the same bus.
I mean, that could just be normal, routine failure to negotiate effectively. If every bus vendor says "call for pricing" and your organisation has "always" paid $940k per bus, when you're told to buy some more buses, you might not even know you can get them for half or a third of that price by getting competing quotes from other vendors.
And if you're an ambitious, hard-nosed type that can really turn the screws on vendors, leaving no stone unturned in your search for savings - would you be working in the purchasing department of a municipal bus company?
Absolutely not. Cost savings is career suicide in the public sector. The goal is to spend all budget and then beg for more. Regardless of ridership, the ironclad rule is "budget must go up".