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?
Government employees are NOT well-equipped to compete with private sector ones; they don't think like them and they don't act like them. Why? Because the public sector is driven by a completely different model: bottoms-up management, led by the citizenry, not led top-down to maximize shareholder value. In addition, because private sector jobs pay 2x+ what the same level in a public sector organization will pay and thus the candidate pool is simply not at the level that you would expect at a similarly sized private sector organization. Because of this flip-flopped model of operation (bottoms-up vs top-down) Public/Private partnerships are NOT equal arrangements and the private sector companies know exactly how to leverage these differences in their favor.
In this instance, a public sector employee may feel that paying more for a bus will better serve the public good because it /may/ be better engineered, have a longer lifetime, and offer value to the public that's above and beyond what a less expensive model will do. But! Even if the support staff look for multiple quotes from a variety of vendors, all of which may be at the cost level a private sector company may prefer, that public sector staff member may very well be directly overruled by the elected officials; who, for reasons that can only be hypothesized (take your pick: corruption, brand/personal preference, whatever) may prefer the more expensive vendors that were not included in the research and bidding process.
While I have laid out that the public sector is not well-equipped for public/private partnerships and business dealings, there are MANY reasons for this including: candidate pool, different underlying model of operation, and elected official decisioning.