My comment is based on the single report substantiating the larger story in the article. I think you ask a reasonable question. Maybe the particular contractor had an axe to grind. Maybe the bookkeeping was a mess but for reasons of incompetence rather than fraud.
I think the larger picture is troubling, but I can also see a scenario where each of the pieces that builds up to that case has a plausible and benign explanation. I don't think there are enough details in this article to conclude one way or the other.
This means someone making $50K would need to buy $1000 worth of Just Mayo or other qualifying unreimbursed expenses.