Material-support cases are just a small fraction of what the Justice Department counts as terrorism prosecutions, and in the larger picture the government is not doing nearly as well. According to the Center on Law and Security at the New York University School of Law, the government has a 29 percent conviction rate in terrorism prosecutions overall, compared with 92 percent for felonies generally.

Image Sheik Omar Abdel Rahman, the blind cleric found guilty in 1995 of conspiring to wage war against the United States. Credit... Fred R. Conrad/The New York Times

In the trial that ended on Monday with a mix of acquittals and deadlocks, the Holy Land Foundation and several of its officials were charged with giving money to Hamas, the militant Palestinian organization designated a terrorist group by the United States in 1995. The Federal Bureau of Investigation started looking into Holy Land in 1993.

Legal experts said it could be hard to prosecute cases in which some of the evidence was quite old. Indeed, much of the evidence had been available to prosecutors in the Clinton Justice Department, and the material support law was enacted in 1996. But those prosecutors did not pursue the matter.

“There are some of these cases that we did not push — certainly aggressively, sometimes not at all — because we were in a different mindset before 9/11,” said Andrew C. McCarthy, who led the 1995 prosecution of Sheik Omar Abdel Rahman, the blind cleric convicted of conspiring to wage war against the United States.

William Neal, a juror in the Holy Land case, complained that the government’s evidence “was pieced together over the course of a decade — a phone call this year, a message another year.”

Instead of trying to prove that the defendants knew they were supporting terrorists, Mr. Neal said, prosecutors “danced around the wire transfers by showing us videos of little kids in bomb belts and people singing about Hamas, things that didn’t directly relate to the case.”