Not sure what you want but try subtracting and looking at absolute value of the difference
diffMatrix = abs(m1 - m2); % Difference of your two matrices.
tolerance = 0.01; % Whatever.
if any(diffMatrix(:) > tolerance)
maxDiff = max(diffMatrix(:))
warningMessage = sprintf('Warning : some elements differ by more than %f (up to %f).', ...
tolerance, maxDiff);
uiwait(warndlg(warningMessage));
end
Adapt as needed.