Perhaps Clattenburg's fiercest criticism in top-flight refereeing followed his officiating of the Merseyside derby between Everton and Liverpool on 20 October 2007.The first notable incident involving Clattenburg was the award of a penalty kick for an apparent professional foul by Everton's Tony Hibbert on Liverpool's Steven Gerrard. Clattenburg initially appeared to take out his yellow card to book Hibbert but after an interaction, albeit brief, with Gerrard, Clattenburg changed his mind and issued Hibbert a red card. He later elected not to send off Dirk Kuyt for a waist-high lunge at Phil Neville.One final controversy arose when he declined Everton's appeals for a penalty in the third minute of injury time, with the score at 1–2, when Jamie Carragher appeared to foul Joleon Lescott in the Liverpool penalty area. Clattenburg was not appointed to referee another Everton match until 2012.
In December 2009, Clattenburg took charge of a tie between Bolton Wanderers and Manchester City. City personnel alleged that at half-time, Clattenburg asked members of their bench: "How do you work with Craig Bellamy all week?" In the second half that followed, he booked Bellamy twice, once for dissent and then for diving, although replays suggested he was actually fouled. City manager Mark Hughes later said: "I've seen Mark Clattenburg have a lot better games than he's had [here today]" and described his decision to send off Bellamy as "laughable".
Clattenburg has also encountered contempt when officiating two fixtures between Tottenham Hotspur and Manchester United. In 2005 when Tottenham's Pedro Mendes had a long-range shot fumbled over the line by United goalkeeper Roy Carroll, neither Clattenburg or his assistants were in a position to award the goal. Five years later, in October 2010, he allowed to stand a United goal scored under controversial circumstances (although strictly correct under game laws) when Nani tapped the ball into the net while Spurs keeper Heurelho Gomes believed his team had a free-kick.
Clattenburg has, however, been the recipient of good feedback from some figures in his recent career. After an incident-filled game between Queens Park Rangers and Nottingham Forest in February 2011, QPR manager Neil Warnock described the official's handling of the match as "absolutely fantastic". Clattenburg issued an early red card to Forest's Radosław Majewski for a two-footed lunge on Adel Taarabt, and he also dismissed QPR appeals for a penalty when Wayne Routledge went tumbling in the box late on. Despite that, and a total of 27 fouls during the game, Warnock praised Clattenburg for being "so in control."
On 28 October 2012, Chelsea lodged a complaint with Premier League stating that Clattenburg had used inappropriate and racially abusive language towards two Chelsea players.