The "Boyhood" actress got a standing ovation by Meryl Streep during the ceremony on Sunday and much praise in the media.
In her answer to a question whether she had seen Streep's reaction, Arquette, 46, said she had not but she later hugged the veteran actress.
She then went on to elaborate on her onstage comments, saying, " ... Even though we sort of feel like we have equal rights in America, right under the surface, there are huge issues that are applied that really do affect women.
The comment sparked an instant reaction on Twitter with many expressing disappointment.
"People of colour have enjoyed freedom for so, so long and yet we continue to ignore the plight of downtrodden Patricia Arquettes. #ashamed," one user wrote.
"Other than disappearing women of color, trans women, and lesbians, Arquette was great," said another.
Arquette later took to Twitter to defend her comments, saying, "I have long been an advocate for the rights of the #LBGT community. The question is why aren't you an advocate for equality for ALL women?
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