Mission Local reports that graffiti scrawled on the window that was not shattered, read "Free Palestine."
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Smitten's owner is Jewish, according to Mission Local.
MORE: San Francisco deals with increasing graffiti, tagging to private properties
San Francisco police found the windows smashed just before 3 a.m. when they went to check out an alarm at the Valencia Street shop.
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Police say this is an active and ongoing investigation.