In the 2007–08 season, Kisnorbo was relegated to League One with the club, but was also on the receiving end of no less than three controversial refereeing decisions. His first was a goal against Scunthorpe United on 20 October, which referee Scott Mathieson ruled out for an offside, depriving Leicester of an away win. Video replay showed that Kisnorbo's disallowed goal was actually onside, greatly frustrating him, while Leicester coach Gerry Taggart commented "We have all seen the replay of Patrick's goal in the dressing room and he is clearly not offside." Kisnorbo's second was a red card by referee Phil Joslin for what the linesman claimed was a foul on Pablo Couñago. Joslin awarded Ipswich Town a penalty kick, and Ipswich won 3–1. Joslin admitted his mistake, and had the ban rescinded the following day after video replays showed Kisnorbo actually won the ball outside the penalty area. Leicester's then-manager Ian Holloway described the sending off as a "complete kerfuffle". The Leicester club was fined £3,000 by The Football Association, however, because of Kisnorbo's teammates' angry appeals to Joslin during the game. Kisnorbo's third was another red card by referee Mike Pike for a foul on Billy Sharp on 5 April 2008. Pike awarded Sheffield United a penalty kick as they won 3–0. Video replays, however, showed no contact between the two, confirming that Sharp was diving. Holloway branded Pike's decision "embarrassing", saying "that was the biggest blunder I've seen in a long time." Leicester also succeeded in their appeal against the second red card.
Further misfortune came when Kisnorbo suffered damaged knee ligaments in 3–1 defeat to Sheffield Wednesday on 26 April 2008, sidelining him for six months. His injury badly affected Leicester's hopes of surviving in the Championship. He played his 100th game and scored his last ever goal for Leicester in a 2–0 home win over Ipswich on 26 December 2007.
Kisnorbo returned to action the following season in a 3–0 reserve team win over Rushden & Diamonds on 2 October. He later returned for the first team coming on as a substitute in a 1–1 draw against Oldham Athletic on 18 October 2008. However, he was struck with another ligament injury to his other knee in a 3–0 FA Cup win over Stevenage Borough on 9 November, putting him out for two more months. Kisnorbo made his competitive return as a second-half substitute in a 1–0 win over Millwall on 14 March 2009, but by then was facing competition in the first team from teammates Wayne Brown, Jack Hobbs, Michael Morrison and Aleksandar Tunchev. He started just three games in the second half of the season, which saw the club secure their promotion as League One champions.