Yes. There have been indictments of individuals for failing to pay taxes on fringe benefits, such as the 2019 prosecution related to multiple instances of fraud including failing to report $410,000 of fringe benefits for People's Express, a bankruptcy start up airline.
Often executives are prosecuted criminally, but corporations are actually easier to obtain convictions against (for example, corporations do not have protections under the 5th Amendment against self-incrimination). But since civil and criminal fines are hard to distinguish, it is more common to seek civil fines than criminal convictions against corporations, while pursuing criminal penalties against key officers and employees of the corporations. The U.S. Department of Justice has a set of policies (also here) regarding when corporations themselves should be prosecuted criminally that have parallels in state prosecutor's offices.
A list of corporate criminal prosecutions in the 1990s (mostly for non-tax violations) can be found here. For example, in 1991, the Georgia Pacific Corporation was convicted of tax evasion and fined $5 million.
Tax fraud prosecutions are rare but hardly unprecedented, although large civil penalties are vastly more common. There is nothing terribly new about it either. For example, an academic article on defending criminal tax prosecutions against publicly held companies was published in 1978.
Simply stealing money meant for employee fringe benefits or taxes on those benefit is a more commonly prosecuted crime.
At the federal level, in 2020, there were 593 tax evasion convictions in the US. In 2019, 848 people were sentenced, and in 2018 — 1,052. 945 prosecutions were recommended for tax crimes in 2020 in the U.S. In 2018, there were 1,050 recommendations. In 2019, the number of recommended prosecutions was 942, and in 2020 — 945.
State tax fraud prosecutions are similarly rare but not unprecedented, although the raw number of cases per year is smaller because the federal statistics cover the entire United States, while state tax fraud cases comes from just one of fifty states.
Almost all tax code provisions are the subject of fraud prosecutions at some point, and the common bond of the provisions is not the nature of the tax code section violated, but the willfulness of the violation. Detailed breakdowns of tax fraud prosecutions by type of tax code provisions violated are hard to determine, without detailed reviews of court records, because they all fall under the same criminal code sections.
Many current federal prosecutions focus on tax fraud related to COVID related tax credits and cryptocurrencies. But federal tax prosecution agencies don't track fringe benefit fraud as a distinct subtype of case, and fringe benefit tax fraud could be variously classified as employment tax fraud, abusive tax schemes, general tax fraud, or corporate fraud.