3 x 3 = 9, which is an odd number. Pairs of x and y positions take two items per pair, which is even. You cannot store an whole number of even values in an odd number of slots without having a slot left over.
Perhaps you want
m = cell(3,3);
and then store (for example)
m{2,3} = [x,y];
This would result in a 3 x 3 cell array, each member of which holds two values. This would not be a numeric array.
