My response might be harsh but tough shit for the company. If the company made a choice to fraud the government, then they should be accountable for their decision. The board of directors is fully responsible for every action of their company including their employees actions as the employee are in capacity and representative of the company. If the employee went rogue/lazy then it is the company due diligence to ensure that every data is verified and correct as the company is still responsible for everything.
They simply can fire the employee and could keep fudging the data. Whelps the company did it again, gee whiz. They can fire the another employee and say it is all good. This mentality is why companies are pushing the boundaries with the governments and still can blame on their employee and get away from the accountability.
That level of accountability is very expensive however - you might find yourself wishing for the good old days when government toilet seats only cost $600.
Are we talking about the same individual? The one named in the article is "Director of Metallurgy". When you're in a position like that, you represent the company, especially for work orders.
ETA: in some ways, the Navy might have reasons to prefer this contractor in the future, because the issue seems to have been caused by a lazy rogue employee and the company seems to have strong enough ethical/internal standards that the Navy can reasonably expect issues to be brought to their attention.