Board Thread:The Reference Desk/@comment-67.159.143.245-20150525014248/@comment-92.232.120.225-20150530125839

You mean in general or at the start of Rise of the Cybermen? For general malfunctions, the engines I believe were damaged by a magno-grab (while the shields were down) in Journey to the Centre of the TARDIS, while the 1996 movie makes vague mention of a timing malfunction causing the Doctor to make an emergency stop in San Francisco while on the way to Gallifrey. Also, in The Name of the Doctor, one of Clara's echoes mentions that the TARDIS' "knackered" navigation system would mean the First Doctor would have more fun stealing that one. According to Journey's End, a fully armed Dalek fleet could disable the TARDIS' shields and trap the TARDIS in a temporal prison.

Also, removing the dematerialisation circuit (from several Third Doctor stories) I believe prevents the TARDIS from, well, dematerialising.