The article carried the headline, 'Terror link group to build London's biggest mosque' and even used pictures of July 7 bombers Mohammad Sidique Khan and Shezwad Tanweer, to illustrate the piece.
Mangera, who was recently featured in the AJ's 40 under 40 list, said he was astonished by the article.
'It's ridiculous. Why would a building like this, which will be a London landmark, have any association to any group? And why did they carry pictures of the London bombers? It didn't make much sense.
'There seems to be an agenda here. This is the first mosque in London to address architectural and community issues through interface spaces, with real sustainability,' he said.
Andrew Gilligan, the article's author, said he knew nothing about the headline and it was subsequently changed for the later West End final edition.
The £100 million project located in West Ham, near the 2012 Olympic regeneration sites, will offer a multi-functional mosque with a school, offices, restaurants and residential accommodation.