The IRS or a state department of revenue may claim a business failed to pay the actual taxes owed based on a variety of reasons, despite good faith efforts. For example, the IRS may allege that a company or its owners reported losses based on a claimed basis which it believes has not been substantiated. Rules governing basis vary on a variety of factors such as the type of entity your own.
In other situations, a state department of revenue may claim a business underpaid sales taxes despite always having used an accountant for its reporting. Such cases can even give way to potential claims against an accountant.
In some cases, a department of revenue can claim that business owners failed to report proper taxes based on the idea that a ‘common enterprise’ exists among a number of their separate business entities.