The West Bromwich Albion striker has been charged by the FA for the sign.
Lukaku featured in a video interview posted on the Toffees' website in which he said there did not have to be "such a big deal" made about the West Brom player's actions.
However, with comment growing on social media, Everton removed the footage when they became aware there was an issue.
"It is the player's opinion and not the opinion held by the football club," Everton's director of communications Alan Myers said.
"We moved quickly to remove any interview that may have been offensive to anyone.
"The last thing we want to do is cause offence to anyone."
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