Małkowski was notable for making a series of errors in derby matches against Hibs' rivals, Hearts. His first two mistakes in the 2006 Scottish Cup defeat, followed by an error leading to a Hearts equaliser in the next derby, which Hibs won 2–1. Having kept his place under Tony Mowbray during the following season, he made two bad errors in the first derby after Mowbray's departure to West Brom. Małkowski's errors resulted in a draw, in a game where they had been 2–0 up after sixteen minutes. In what proved to be Malkowski's last game for the club, he made a serious error in the next derby match, when he dropped a tame free kick by Paul Hartley into the path of Edgaras Jankauskas, who scored into the unguarded net. This led to Małkowski being dropped from the Hibernian squad entirely for the following match against Dunfermline, being replaced by Andrew McNeil.