From the OED
Etymology: Etymology unknown.
a. A surge of current or a spurious electrical signal (see quots.); also, in extended use, a sudden short-lived irregularity in behaviour.
b. Astronauts' slang. A hitch or snag; a malfunction.
1962 J. Glenn in Into Orbit 86 Another term we adopted to describe some of our problems was ?glitch?. Literally, a glitch is a spike or change in voltage in an electrical circuit which takes place when the circuit suddenly has a new load put on it... A glitch..is such a minute change in voltage that no fuse could protect against it.