1. He is reported as urging 'students to wage jihad in Palestine. In a clandestinely recorded speech, Begg said to students: "You want to make jihad? Very good...Take some money and go to Palestine and fight, fight the terrorists, fight the Zionists."' (source) This has been strongly denied by the Federation of Student Islamic Societies:
“Some of the comments that have been attributed within the article, have been deliberately taken out of context to push a certain viewpoint, rather than present a balanced picture. An example of this was the misquotation of Imam Shakeel Begg who was actually delivering a talk on the illegitimate nature of terrorist activites that have taken place in recent years, which was overlooked by the article."2. He says the veil is not a subject for free speech within the Muslim community.
The veil, irrespective of its specific juristic rulings, is an Islamic practice and not a cultural or a customary one as is agreed by the consensus of Muslim scholars; it is not open to debate...3. On the other hand, he thinks the fascist Hizb ut-Tahrir are entitled to free speech, their "extremism" simply an unhelpful, emotive pejorative term; their support for "terrorism" simply support for "the right of people anywhere in the world to resist invasion and occupation". (source)
We recognise the fact that Muslims hold different views regarding the veil, but we urge all members of the Muslim community to keep this debate within the realms of scholarly discussion amongst the people of knowledge and authority in the Muslim community. (emphasis added. source)
4. He endorses the Tayyibun Institute, dedicated to the spread of Islamic ultra-orthodoxy, which in turn endorses the (alleged) terrorist fundraising group Interpal, favourite charity of George Galloway (of "Celebrity Big Brother" infamy).
[UPDATE May 24 2013: I have written more about the Lewisham Islamic Centre here, talking the story up to 2013, in light of alleged link of Michael Adebolajo to the Centre.]