As @Star Strider says, categorical variables are not ordinal by default and are valued by lexical sorting. To fix
X = {'Pristine' 'Ne' 'He' 'Ar' 'Kr'};
X=categorical(X,X,"Ordinal",1)
hB = bar(X,E,'stacked');
...
Produces
in which the order is preserved since X is now an ordinal categorical array.
You can generalize the above by using sort with the optional returned index array by which to reorder the categorical values array to match the data order desired or for different datasets before creating the categorical variable.
