Workers pulled smoking glassware from the pit at the Spring Valley neighborhood site, said project manager Dan Noble.
Engineers suspended digging April 8 as a precaution.
Preliminary tests show the glassware was contaminated with the toxic chemical arsenic trichloride. Officials will review safety procedures before digging continues.
Workers also discovered the chemical agent mustard in a jar. It was used as a weapon to cause blisters, breathing problems and vomiting.
"It’s a much larger disposal area than we predicted," Noble said.
During World War I, the Army used the university as an experiment station to develop and test chemical weapons.
This is the fourth major dig for munitions and toxic agents over the past 16 years since burial pits were discovered in the neighborhood.
The cleanup project is one of the only places in a major city classified by the Army Corps as a “formerly used defense site.”