The name of "Arthur Misty Thackeray", Ukip's top official north of the Border, appeared on the petition but he denied all knowledge of the steward.
The Sunday Herald last week revealed that Thackeray had made a series of offensive posts on Facebook on religion.
In 2011, he wrote: "Real Catholicism and Real Islamism are far from antagonists with both having an outwardly benign image but inwardly sharing a fascist ideology of extreme submissive conservatism and imperialism ..."
He also took aim at Holyrood: "[T]here's more chance of winning the lottery two weeks running than getting an openly Rangers-supporting MSP into the chamber of the institutionally catholicised pretendy parliament .. lol." Thackeray, who works in the security industry, also made claims about Glasgow City Council's policy on marches: "No wonder the blue half of my city say G.C.C actually stands for the Glasgow Celtic Council for Gays Catholics Communists eh.lol. NS!"
The comments prompted Jonathan Stanley, a senior Ukip member in Scotland, to urge him to attend an anti-sectarianism course.
Thackeray is now facing questions over an online petition about a steward who was sacked by Middlesbrough FC due to far-right political activity. The petition was started by a one-time BNP candidate and read: "We the undersigned petition Middlesbrough Football Club to reverse their decision in sacking Barry Towers for standing in the local council elections for the British National Party."
The name Arthur Misty Thackeray is on the petition, as are more than 200 other names.
SNP MEP Alyn Smith said: "Mr Thackeray needs to answer questions on why his name appeared on this petition. The people of Scotland have a proud tradition of supporting justice and tolerance; it is for this reason that Ukip will continue to be rejected at the polls north of the Border."
Thackeray said: "The only Barry Towers I'm aware of is a high-rise block in Wales."
He said the suggestion he had signed the petition was "ridiculous", adding: "I am well aware a Walter Mitty character is feeding misinformation to anti-Ukip and pro-separation media outlets to demonise and destabilise myself and the party."