Bourrienne in Hamburg is always a good one to reference. He was sacked and fined.
If you would like others, perhaps you could actually go into Napoleon's Correspondence for the wealth of information to be found there. Or, perhaps, investigate Eugene's Correspondence also, as he was particularly harsh with inefficient administrative officers and Napoleon would back him up if asked. Berthier would also act against 'official looting' by French general officers, such as Bernadotte's chief of staff who had 'procured' 5,000 pairs of shoes from one of Davout's depots and General Mahler who had claimed money 'procured' from an occupied city was a 'gift.'
When Lannes overspent on the uniforms of the Consular Guard, Napoleon told him he'd have to make it up out of his personal funds or be cashiered. Luckily for Lannes, Augereau loaned him the money to make it up. That wasn't fraud, but it was the misuse of funds, per se, and Napoleon was death on that subject. Napoleon was serious about 'honoring the public trust' regarding funding.
Undoubtedly, by the tone of your 'question', you don't believe that Napoleon would prosecute dishonesty among his higher-level officials, or from his general officers, but there would be no other point in establishing an office or group of auditors if he wasn't serious about it.
However, it is not a usual pursuit of mine, historically, to study an issue such as this but merely have run into it in my studies.
If you don't agree with my conclusion, perhaps you can demonstrate why...?