According to the court documents, Tony Drakes, one of the witnesses the students believe was involved in the 1978 murder of security guard Donald Lundahl, told state investigators that he "gave the students a video statement for money" and recanted the videotaped statement.
In the prosecutors' documents, Drakes alleges that Sergio Serritella, the private investigator working with the students, gave a taxi driver $60 for what was estimated to be a $6 cab ride home to a bus station near where the 2004 interview took place.
Drakes says the the cab driver gave him "the change" -- about $40 -- which Drakes says he later spent on crack cocaine.
Protess said a student did give the cab driver money, but argued that his students and Serritella were following "journalistic practice" in helping a source get home safely from an interview.
"What we have control over is getting the receipt from the cab driver that he is the one who was given the money," said Protess. "What happened to the money afterward we have no control of."
Records from the cab company are included in Tuesday's filings and show that the cab driver was, in fact, given the money. Drakes, referring to the students as "snotty and manipulative" in conversations with state investigators, has since recanted the videotaped testimony that he gave to the Northwestern students in which he said McKinney was not even present the night the security guard was killed.
Another witness, Francis Drakes, Tony Drakes' nephew, initially told police that Tony Drakes admitted the security guard's murder, according to the court documents filed Tuesday. But the documents reveal that he also later told investigators that the female students who interviewed him "flirted with him" and "flattered him" during the interviews.
He went on to say his testimony that implicated Tony Drakes in the murder was "a story" that he gave the female students so they would stay with him longer. Francis Drakes is currently in jail on an unrelated murder conviction.
The prosecutor's office admits in court documents to paying another witness, Michael Lane, $10 for gas after their interview.
Protess suggests giving the money directly to a witness might be worse than giving it to a cab driver.
"What's worse?" asked Protess. "Giving money directly to a source or paying a cab driver to take the source from an interview? They are certainly the pot calling the kettle black."
The prosecution's spokeswoman Daly called Protess' analogy "ridiculous."
"We did not pay for any interviews or statements," said Daly, "Nothing of that nature, unlike what apparently happened with the students and the investigators."
The university's lawyer, Richard O'Brien, told ABCNews.com the Cook County's prosecutor's office is wrongly focusing attention on the students' records and could jeopardize future investigations. The school worries that turning the legal microscope on the students could deter future students from participating in the Innocence Project.
The school's lawyers have until Jan. 11 to respond to the prosecution's latest request.