Your legend is showing the first four objects you plotted, which is bar, scatter, bar, scatter. You're only giving it 4 legend entries instead of 8, so I'm assuming you want only the bar or the scatter to show.
I'm not sure if you want the scatter plots to show in the legend or the bar plots, but whichever ones you want hidden from the legend, put 'HandleVisibility', 'off'. E.g. plot(x,y,'HandleVisibility', 'off').
I don't have access to your data, but here's an example:
barDat = [3 5 1];
scatterDat = [1 2 3; 4 5 6; 7 8 9];
cols = {'red','cyan','green'};
names = {'1','2','3'};
figure()
for ii = 1:length(barDat)
bar(ii,barDat(ii),'FaceColor',cols{ii});
hold on
scatter(repmat(ii,size(scatterDat,2),1), scatterDat(ii,:),'k','filled','HandleVisibility','off')
end
l = legend(names);
