After the 2009 Manchester derby at Old Trafford, Atkinson was criticised by Manchester City's then-manager Mark Hughes for bad time-keeping after Manchester United had scored an injury-time winner. The fourth official had signalled four minutes of additional time, but Michael Owen scored a 96th-minute goal, handing United a dramatic 4–3 win.
In September 2010, Atkinson was handed a one-week demotion to the role of fourth official after a time-keeping dispute with Everton manager David Moyes. Everton had scored two injury-time goals to make the score 3–3 against Manchester United, but Atkinson then blew his final whistle while Everton were midway through an attack with a chance of a winner.
In September 2010, Atkinson was handed a one-week demotion to the role of fourth official after a time-keeping dispute with Everton manager David Moyes. Everton had scored two injury-time goals to make the score 3–3 against Manchester United, but Atkinson then blew his final whistle while Everton were midway through an attack with a chance of a winner.

