When officers arrived in riot gear, protesters started throwing bottles and other projectiles, according to authorities, and some of the objects were pelted at officers, which prompted an order to disperse.
When some groups failed to leave the area, less-than-lethal force was deployed.
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The viral video from the scene shows one officer firing the rubber bullet, hitting one of the protesters in the stomach. She is seen on camera falling to the ground. The woman's condition was not immediately available.
The Los Angeles Police Department has not released a statement about the incident, which is raising questions about the officer's use of force.
Law enforcement expert Bruce Thomas doesn't understand what prompted the use of that weapon.
"There were some projectiles that were being thrown at the police. They did recover some weaponry, that kind of thing," Thomas said. "But in this case, I just didn't see an exigent circumstance for the use of less-than-lethal by this officer."
LAPD sends alert warning of unlawful assembly, ordering crowd to disperse during K-town spa protest
A total of 40 people were arrested, 39 of which were for failure to disperse and one for bringing a "prohibited item" to a protest, according to the department.
The exact nature of that item was not disclosed, but the department on Saturday said "numerous weapons," such as knives and mace, were found on the ground where the arrests were made.
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The demonstrations, similar to previous incidents outside the Wi Spa in the 2700 block of Wilshire Boulevard, were apparently fueled by the spa's policy to accept transgender customers.
A protest earlier this month was sparked by a viral video posted by a woman upset that a person who identified as female was allowed to disrobe in the women's section of the spa.
Wi Spa defended its policy in a statement to Eyewitness News, which reads in part: "Like many other metropolitan areas, Los Angeles contains a transgender population, some of whom enjoy visiting a spa. Wi Spa strives to meet the needs and safety of all of its customers, and does not tolerate harassment or lewd conduct by any customer, regardless of their sex, gender, or other characteristic."