Your xlimits are only showing one of the box plots. I'd also recommend using yyaxis here or perhaps subplots.
X1= [1.2 2.2 3.2 4.2 5.2];
X2=[1.4 2.4 3.4 4.4 5.4];
X3=[6.2 7.2 8.2 9.2 10.2];
X4=[6.4 7.4 8.4 9.4 10.4];
A=rand(100,10); % Data
B=rand(100,10)+5; % Data
f=figure;
yyaxis left
hold on
BoxA = boxplot(A(:,1:5),'positions',X1, 'width',0.18,'notch','on','color','r');
set(gca,'XTickLabel',{' '})
BoxB = boxplot(A(:,6:10),'positions',X2, 'width',0.18,'notch','on','color','b');
set(gca,'XTickLabel',{' '})
yyaxis right
BoxC = boxplot(B(:,1:5),'positions',X3, 'width',0.18,'notch','on','color','r');
set(gca,'XTickLabel',{' '})
BoxD = boxplot(B(:,6:10),'positions',X4, 'width',0.18,'notch','on','color','b');
set(gca,'XTickLabel',{' '})
xlim([0 12])
