First, notice that in Matlab a=[ [1 2], [2 3], [4 5] ] equals a=[1,2,2,3,4,5]. I guess, you meant to associate each entry of mean=[5.43, 6.78, 5.66] with one coordinate couple (x,y) in a.
To do that, just define your X and Y and plot mean against them:
X=[1,2,4];
Y=[2,3,5];
mean=[5.43,6.78,5.66];
plot3(X,Y,mean,'*');
grid on;
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