Chelsea was in attendance at a vigil in New York University after gunman, Brenton Harrison Tarrant, attacked the two mosques, wanting to just pay her respects to the victims.
"This [vigil] right here is the result of a massacre stoked by people like you and the words that you put out into the world", said the activist, a young woman.
The caption and comments were an apparent reference to Ms Clinton's condemnation of Democratic congresswoman Ilham Omar, who was widely criticised last month for using "anti-Semitic tropes".More news: 10 mins before attack, New Zealand mosque attacker mailed manifesto to PM
Clinton never did say anything hateful about Muslims, nor did she attack Muslims in any way.
Donald Trump Jr. took to Twitter Saturday to defend Clinton, saying the incident was sickening, and everyone should be condemning anti-Semitism and all forms of hate. Omar's comments were widely criticized by members of both political parties, and she eventually apologized and deleted the tweet. "I believe we have to show solidarity with each other". "I want you to feel that deep inside, that forty-nine people died because of the rhetoric that you put out there".
"I am so sorry that you feel that way", Clinton told the students. The son of President Donald Trump, 72, didn't hesitate to speak his mind in his tweet and even suggested praise for Chelsea.More news: Blazes, looting hit Paris as Gilets Jaunes seek new momentum
"What does 'I'm sorry you feel that way mean?'", someone from behind the camera yells, before the video cuts out. "Anyone who doesn't understand this is part of the problem".
"Chelsea Clinton was trying to speak out against bigotry and her words were used to claim she was a bigot", said journalist Tim Pool.
Former Arkansas Governor Mike Huckabee, a prominent conservative commentator, agreed and said the blame lies exclusively with the gunman. "We should expect all elected officials, regardless of party, and all public figures to not traffic in anti-Semitism", Chelsea tweeted about Omar's accusation.More news: Chaotic scenes as Nigel Farage leads 'Brexit betrayal' march
Journalist Michael Weiss sarcastically offered: "Seem to have missed the Chelsea Clinton connection to the New Zealand attack".
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