This year isn't shaping up to be any better for Jonathan Gruber than 2014 was. An audit of work done for the state of Vermont by the controversial Obamacare architect found that he may have overbilled for the job. The audit is the latest in a series of black eyes for Gruber, who in a video that came to light last year was seen talking about how the "stupidity of the American public" allowed Obamacare to be passed into law.

The Vermont audit, which cites Gruber's "inconsistencies and questionable billing practices," also faults state officials for failing to exercise sufficient oversight over the MIT economist's invoices. The audit has been referred to Vermont's Democratic attorney general, William Sorrell, who reportedly said it raises "serious questions."

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Gruber's billing came in connection with a $400,000 contract for research and modeling work related to Vermont's since-abandoned plan to implement a single-payer health-care system for state residents. State Auditor Douglas Hoffer's inquiry found that Gruber's first invoice for hours worked reported "round numbers"—100 hours for him, and 500 hours for his research assistants—which Hoffer noted is "possible, but unlikely." Hoffer also pointed out that the "plain language" of Gruber's contract did not allow him to bill in round numbers. Read MoreHatch promises subsidy 'solution'

"The second invoice reported exactly the same figures, which is implausible," Hoffer wrote. The auditor further noted that Gruber used only one research assistant during the period billed for, and "it seems unlikely that the RA could have worked 1,000 hours in 10 weeks," which was the total in the two invoices. And, Hoffer said, a December invoice submitted by Gruber includes hours he worked, "which is expressly forbidden by" the contract as it was amended in November. "The evidence suggests that Dr. Gruber overstated the hours worked by the RA and that the Agency of the Administration ignored the obvious signs that something was amiss," Hoffer wrote. Gruber declined to comment on the audit when contacted by CNBC.com