The code you have is explicitly setting the positions of the axes to be the same (i.e., each axes in one set of three axes has the same position as an axes in the other set of three axes). To fix that, figure out what the positions need to be instead. Something like this maybe:
% dummy data
XMesh1 = [0 1];
YMesh1 = [0 1];
ZMesh1 = [1 2; 3 4];
f = [1 2];
xi = [0 1];
yi = [0 1];
XMesh2 = [0 1];
YMesh2 = [0 1];
ZMesh2 = [1 2; 3 4];
%% Plot #1
figure;
ax1 = subplot(1,2,1); % NB: this is ax1, I assume
% Main plot
contourf(XMesh1,YMesh1,ZMesh1,2,'EdgeColor','none') % NB: using 2 contours, not 10000 here
xlabel('X (Degree)'); ylabel('Y (Degree)')
ax1.Position=[0.1,0.1,0.25,0.6];
ax1.TickDir='out';
% X Axis histogram
ax2=axes('Parent',gcf);hold(ax2,'on')
% [f,xi]=ksdensity(X_GS);
fill([xi,xi(1)],[f,0],[0.34 0.47 0.71],'FaceAlpha',...
0.3,'EdgeColor',[0.34 0.47 0.71],'LineWidth',1.2)
ax2.Position=[0.1,0.75,0.25,0.15];
ax2.YColor='none';
ax2.XTickLabel='';
ax2.TickDir='out';
ax2.XLim=ax1.XLim;
% Y Axis histogram
ax3=axes('Parent',gcf);hold(ax3,'on')
% [f,yi]=ksdensity(Y_GS);
fill([f,0],[yi,yi(1)],[0.34 0.47 0.71],'FaceAlpha',...
0.3,'EdgeColor',[0.34 0.47 0.71],'LineWidth',1.2)
ax3.Position=[0.375,0.1,0.075,0.6];
ax3.XColor='none';
ax3.YTickLabel='';
ax3.TickDir='out';
ax3.YLim=ax1.YLim;
%% Plot #2
ax1 = subplot(1,2,2); % NB: this is ax1, I assume
% Main plot
contourf(XMesh2,YMesh2,ZMesh2,2,'EdgeColor','none') % NB: using 2 contours, not 10000 here
xlabel('X'); ylabel('Y')
ax1.Position=[0.6,0.1,0.25,0.6];
ax1.TickDir='out';
% X Axis histogram
ax2=axes('Parent',gcf);hold(ax2,'on')
% [f,xi]=ksdensity(X_G);
fill([xi,xi(1)],[f,0],[0.34 0.47 0.71],'FaceAlpha',...
0.3,'EdgeColor',[0.34 0.47 0.71],'LineWidth',1.2)
ax2.Position=[0.6,0.75,0.25,0.15];
ax2.YColor='none';
ax2.XTickLabel='';
ax2.TickDir='out';
ax2.XLim=ax1.XLim;
% Y Axis histogram
ax3=axes('Parent',gcf);hold(ax3,'on')
% [f,yi]=ksdensity(Y_G);
fill([f,0],[yi,yi(1)],[0.34 0.47 0.71],'FaceAlpha',...
0.3,'EdgeColor',[0.34 0.47 0.71],'LineWidth',1.2)
ax3.Position=[0.875,0.1,0.075,0.6];
ax3.XColor='none';
ax3.YTickLabel='';
ax3.TickDir='out';
ax3.YLim=ax1.YLim;
