...always nice to see that Martin-Baker equipment works as advertised, but the primary question remains as to why the CF-18 "system" failed in this mishap. After all, the primary purpose of this entire flyby/demo operation was to publicly show how great that CF-18 system works.
Video of the mishap is brief but revealing. It shows a low speed runway pass at very low altitude, with a smooth transition to a classic asymmetric stall (right wing drop) and a right yaw before nose low impact.
The aircraft stalled because it was flying too slow for those conditions. Lack of adequate speed might have been a piloting problem or some aircraft malfunction. A clean F-18 normally has lots of thrust available and flys well even on one engine.
Differing engine nozzle configurations seem abnormal. Spectators report that one afterburner engaged just prior to impact, and the impact video section indicates the left engine might have been in AB. A malfunction on one engine could account for all that, but absent any other obvious problems (smoke/fire, aircraft oscillations, etc) it seems a lower probability. Bird-strike is also possible, but likely would have been noticed by the many spectators.
It's also possible the pilot had one engine in idle and controlling thrust entirely with the other throttle... perhaps to demonstrate CF-18 single-engine capability (as part of the formal flyby practice, or merely to himself). That would account for nozzle difference and sudden use of only one AB (..and the quick yaw just before impact).
Getting behind-the-Power-Curve at low altitude can be big trouble, even for modern high-performance jet fighters.
Also, early flight testing (mid-1990's) of F-18E/F revealed a significant aerodynamic problem -- sudden uncommanded "wing drop" (asymmetric stall) during certain maneuvers; physical wing modifications corrected the problem... but perhaps the CF-18 has some similar behavior in unusual circumstances ?