"I am stunned, stunned because it's always sad when somebody, regardless of what the reasoning is, resorts to putting any kind of symbol out there that depicts some kind of hatred," Santee Mayor John Minto said.
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It happened at a Vons grocery store in Santee, California, which is located in San Diego County.
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A shopper who took photos of the man in the KKK hood said employees at the store told the man to remove the hood or leave.
The images sparked outrage online and from community leaders.
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"Pictures like that are always shocking," said Tammy Gillies of the San Diego Anti Defamation League.
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Law enforcement was not called to the scene, but San Diego County Sheriff's Department said it has opened an investigation into the incident.
"Santee is not about that. We don't condone that. And, and it's just a sad reminder of how people can be intolerant," Minto said.