Faults in complex systems such as Wave Energy Converters (WECs) are inevitable. WECs are expected to work in harsh environments to produce more power which increases the possibility of major failures. Increasing the reliability of WECs calls for the development of early Fault Detection (FD) algorithms which needs understanding of the enormous modes of failures to prevent the costly downtime of the device. Through this work, a methodology is provided to simulate the effect of malfunction with various levels of complexity dependent on time and velocity of the WEC. The fault signals are applied to an experimentally validated model of an array of flap-type WECs. The assumed failures range from the delayed responses to the complete blocked hinge. It is shown that even a signal of soft fault with 7% change in the response amplitude can change the period of the system. These changes are investigated for the development of a general FD algorithm for WECs.