Only one show in Phish history is known to have been cancelled: 7/19/93, at Pier 6 in Baltimore, due to lack of sales (!).
There are some reports that a show was scheduled for the Tree Cafe in Portland, for which, when fans arrived they found the doors bolted shut with an eviction notice saying the club was closed. But that was reported as 1988 or 1989, and Phish played Tree Cafe in 1990.
One Trey Anastasio Band performance was cancelled, as a result of the 10-9-11 Langerado Music Festival being cancelled.
Several other shows have been lacking full personnel but continued anyway. Trey was responsible for the “Guitar Player Taking a Leak” jam at Laguna Seca Daze in ’94, although the band covered with a funny little ditty in classic Phish humor followed by a smoking two-song second encore. Contrarily, Fishman (as told in the “bear story” 3/17/91) missed two of three sets on 7/30/88, gone missing on a bear-scared acid trip, leaving the others to tool around on jazz standards with Trey on drums. For related stories - such as venue- and weather-impacted shows - see the blog post Bad Moments in Phishtory.