Basically, you don't need the second input(), after the inner while loop, at all.
close all, clear all, clc;
% Ask user for size of matrices where [A] = M x M
m = input('What is the value of m, where matrix [A] = m x m? ');
% Create matrices [A]
A = zeros(m,m);
y = 1;
while y < m+1
x = 1;
while x < m+1
i = input(sprintf('Matrix A - input value of row %d column %d: ', y, x));
A(y,x) = i;
x = x+1;
end
y = y+1;
end
A
