Well, you have good data, that's what your overlapping errorbars show. And that's why you show them. If all your data would be like your measurements for 0, 2.5 and 7.5 you could write " Error bars were on the scale of the symbols and are not shown." But in your case you have some visible error bars for the other measurements, so I think its just fine to show them.
You could do it like this
x = X(:,2); y = X(:,1);
y_groups = {};
x_unique = unique(x(:))';
for x_u= x_unique
y_groups{end + 1} = y(x_u == x);
end
my = cellfun(@(x) mean(x), y_groups);
sy = cellfun(@(x) std(x), y_groups);
plot(x, y, '.r')
hold on
errorbar(x_unique, my, sy, 'ks')
