In 2004, Trooper was the main force behind the ban of Rabbi Nathan Slifkin‘s books. Rabbi Slifkin explores in his books conflicts and resolutions between traditional Judaism and modern science. 
In 2006, Tropper revoked the conversion of a woman on the basis of her being seen wearing pants and not covering her hair, thus rendering her children non-Jewish, as well. 
In February 2009 it was revealed on the Daat Torah blog  that a letter  which in several ultra orthodox rabbis strongly criticize rabbi Herbert Bomzer, a modern orthodox rabbi, was forged by Tropper. After the forgery was discovered, some of the rabbis which their names were used in the forged letter released a statement  distancing themselves from it.
In October 2009, Tropper was sued by philanthropist Guma Aguiar for allegedly misappropriating funds given to Tropper by Guma for charitable purposes. The lawsuit followed an altercation between Guma and Tropper in a Jerusalem hotel.