anomaly
Meaning: something that does not fit into the normal order
Usage: “That rip in the space-time continuum is certainly a spatial anomaly,” said Spock to Captain Kirk.
pathology
Meaning: a deviation from the normal
Usage: Dr. Hastings had difficulty identifying the precise nature of Brian’s pathology.
discrepancy
Meaning: difference, failure of things to correspond
Usage: He was troubled by the discrepancy between what he remembered paying for the appliance and what his receipt showed he paid for it.