There's already people out there speculating that something might have gone wrong with the raptor engine towards the end as the exhaust could be seen turning bright yellow, not a color you're supposed to get when burning methane...
The plume also seemed yellow while close to the ground on liftoff. I think it has more to do with the shape of the plume as it’s affected by the exhaust being forced out perpendicular to the direction it left the engine. That’s pure speculation but since the color is the same at liftoff and landing, I think it’s reasonable.
Could also be related to high thrust settings. Landing requires more thrust than hovering, and you can see the plume turn yellow as the hopper starts to decelerate.
It might be unburnt methane. Methane flames do turn yellow-orange in a fuel rich environment. As Methane is lighter than Oxygen, a slightly fuel rich mixture would also make sense for optimum efficiency.
The exhaust looked quite 'normal' on lift-off with the usual relatively colorless aspect of an optimum methane/oxygen ratio and its characteristic Mach diamonds. It only goes yellow towards the end, and suddenly so.
In this particular instance, landing doesn't require more thrust than going up or hovering as there is little deceleration to do. By that stage, the hopper would have been lighter as most of the fuel and oxygen would have been burned and they would have had to throttle the engine to a lower setting. I also believe, as proposed above, that the lower thrust likely probably calls for a different fuel/oxygen mixture due to the particularities of the close-cycle setup. They might need to keep it rich at low thrust for cooling or other intrinsic limitation of the design.
At least I hope, as one of the possibilities would be the engine starting to eat itself from the inside
There's also the apparently heavier than intended landing and the tank that came flying off after said landing. Although given the rather (almost literally) agricultural nature of that test article and its disposable design, that may be within the 'semi-intended' consequences.
I'll do my own airline. With Blackjack. And hookers. In fact, forget the airline.