A Calgary prosecutor says she was asked to deal with outstanding charges against a key Crown witness in the Dustin Paxton torture trial in a quick matter before he was scheduled to appear as a witness.

Margot Engley testified at a stay of proceedings hearing Thursday in a Calgary courtroom, where Paxton's defence team is trying to prove the 31-year-old didn't get a fair trial.

Paxton is accused of physically and sexually assaulting his former roommate and business partner over an 18-month period starting in October 2008. The alleged victim cannot be named under a court order.

Engley told the court she refused to handle the file given to her by Crown prosecutor Joe Mercier on the charges facing Robert Cannon because she thought it should be dealt with by an another prosecutor. She said there is a protocol to follow when dealing with a Crown witness.

Cannon was flown to Calgary by the prosecution in exchange for his testimony against Paxton.

The defence team alleges a special deal was in place to take care of Cannon's outstanding charges, which is part of the reason they applied for a stay of proceedings hearing as the nine-week trial came to a close.

The defence claims Paxton's charter rights were violated because of allegedly late disclosure of evidence and the handling of Cannon as a witness.

If the stay application is granted, the legal proceedings against Paxton would be halted, although the decision could be appealed to a higher court.

Actions of detective in gallery questioned

Two other witnesses testified Thursday that they saw a Calgary police detective direct and signal to Cannon while he was testifying in court.

Calgary lawyer Ola Malik, an observer at the Paxton trial, says he saw a man in the public gallery signal to a Crown witness during cross-examination. CBC

Calgary lawyer Ola Malik said he sat in the courtroom as a curious observer and what he witnessed during Cannon's testimony was "concerning and disturbing."

Malik testified he saw a "bald man" in the back row of the gallery nod and shake his head while Cannon was being cross-examined by Paxton's lawyer, Jim Lutz.

"It was so distracting, it became a pattern," said Malik.

The man also gestured with his hands after the defence lawyer asked the witness to describe how wide a door had been propped open, Malik said.

Malik described the man's body language as overt and exaggerated.

CBC reporter Bryan Labby said video from that day in court was played at the hearing and showed the officer nodded at times, but a hand gesture he made could have been him reaching for a phone.

The Crown said the officer's "nodding" could have been due to checking a BlackBerry or looking at the stack of papers in his lap, adding it was unclear what he was doing. The Crown also pointed out there were several occasions where the detective failed to engage Cannon in eye contact during his testimony.

Earlier Thursday, court clerk Paula Lorenz testified that she saw the detective nodding and shaking his head up and down, to the right and left in large movements.

She said it happened during three separate occasions over an eight-minute stretch.

On cross-examination, Lorenz said she didn't notice anything until it was brought to her attention by Paxton's lawyers. She also said the detective had a notebook with him and didn't maintain eye contact with the witness.

Lorenz said she was concerned about what she saw, but admitted she never told the prosecutor and waited six weeks to tell her supervisor.

The man in the gallery has been identified as Det. Steve Harris, and he's expected to be called as a witness at the hearing.

More witnesses are expected to testify Friday at the hearing, which could continue into next week.