One of the major drivers for using friction stir welding for aluminium fabrication is the low incidence of weld flaws compared to that produced by conventional arc welding. However, the process does have its own characteristic flaws. A number of different process variables affect the quality of a joint produced by friction stir welding: tool design, tool rotation and travel speeds, tool heel plunge depth and tilt angle, welding gap, thickness mismatch and plate thickness variation. Successful, reproducible welds may be produced by operating within process "windows". However, problems may arise when the welding conditions deviate from the standard operating window. In such circumstances, flaws may be generated. In the current work, a number of flaws encountered in friction stir welds, in particular voids, joint line remnants and root flaws were generated in an Al-Cu-Mn-Si-Mg alloy by using welding parameters outside of the established tolerance box for producing flaw-free welds. The welds were characterised using X-ray and ultrasonic non-destructive testing techniques and by metallographic sectioning. The causes of such features are described and recommendations are made to prevent their occurrence.