During the second day of arraignment proceedings at Boston Municipal Court Wednesday for those arrested during the “straight pride” parade, a transgender woman says Judge Richard Sinnott referred to her chosen name as an “alias” and misidentified her using incorrect pronouns.

Defendant Kai De Jesus was arrested during Saturday’s counter-protest and charged with disorderly conduct. De Jesus was one of hundreds of counter-protesters opposing the message of the parade, which suggested that straight people are oppressed majority.

Since De Jesus had no priors, prosecutors moved to nolle prosequi, or discontinue prosecution against her.

“The clerk was using my dead name and "he/him" pronouns, and my attorney explained that she would be using my chosen name, Kai, as well as my female pronouns, she/her/hers, and said she wished to express it to the court so there would be no confusion later on,” De Jesus said. “The judge then said, ‘so this is an alias.’”

De Jesus says Sinnott pushed back on the request to use her chosen name, continuing to refer to it as an “alias,” and asked that the "alias" be run through a separate background check for priors within the system.

“My attorney tried to push and say no, there would be no legal document under this name, but the judge pressed on,” De Jesus said.

De Jesus says she waited in court for the background check process on her chosen name. “My court time was 9 a.m. and it was just pushed back and pushed back,” she said. “I didn't get to leave until it was almost 3 o'clock.”

In a second hearing over five hours after she arrived in court, the check for prior arrests cleared, and the charges were dropped.

“It was a major win and I was very happy, but it felt unsettling and disappointing and stressful, and perhaps even traumatic,” De Jesus said. “You can clearly see from the document that this is not a name I legally use, and if I had priors they would be under my legal name.”

De Jesus, a freshman at Harvard University, says she has not yet legally changed her name due to a “convoluted” legal process.

She says she felt disrespected by Sinnott in the courtroom. “I felt treated unfairly when the judge explained, condescendingly, ‘apparently Miss De Jesus has an alias — and have we run that yet?’ And it was just very uncomfortable and unsettling.”

According to retired federal judge Nancy Gertner, Sinnott is not legally obligated to refer to a defendant by their legal name in a courtroom.

“The judge has the discretion I suppose to call it an alias,” she said. “It is disrespectful to the defendant, but it's certainly the judge's discretion to do that...it’s an issue of how he's running his courtroom. It's not a way that others would have done it but he certainly has the discretion to do that.”

Gertner, who has criticized Sinnott for his decision to move forward with arraignments in cases where the prosecution recommended dismissing charges, says Sinnott’s decision to not accept De Jesus’ pronoun may be interpreted as a sign of bias.

“If someone doesn't change her name legally and says my pronoun is "she," a judge is not obligated to accept that,” she said. “Certainly, the failure to accept it may raise questions about bias and the appearance of bias. The lawyer could then say, ‘well this is a judge who seems to be biased against my client,’ and try to disqualify him.”

De Jesus’ case was filed as nolle prosequi, which District Attorney Rachael Rollins described in a statement as the “absolute power of the Commonwealth” to halt prosecution.

Though most of these types of cases, including De Jesus’, were essentially dismissed, Sinnott rejected others. In response, Rollins to submitted an emergency petition Wednesday to the state’s Supreme Judicial Court calling on the SJC to force Sinnott to accept the nolle prosequi decisions.

In a statement, Rollins described her petition as "a call for order to be returned to our courts," describing Sinnott's actions as “unprecedented and outrageous."

Sinnott’s office did not respond to requests for comment.

Tori Bedford is a reporter at WGBH News