How? It's not that complicated. He didn't pay the taxes owed.
On his own personal taxes, he did not file tax returns and did not report income. He seems to have done this for most of his adult life, but for a three year period... "On July 7, 2006, the
United States Tax Court found that Hovind was deficient in paying his federal income taxes in 1995–1997, totaling $520,099."
In the more recent trial, he was paying employees under the table, and not paying their employment and social security taxes. For the three years covered by the charges... "The first 12 counts were willful failure to collect, account for, and pay over federal income taxes and
FICA taxes, totaling $473,818 for the 12 fiscal quarters of 2001–2003."
So for just the years that were covered by the legal actions, it totals $993,917.