I understand that you want to find the difference between two rows. NaN values are not considered equal, and the logical inequality test, (NaN ~= NaN), also returns true. The documentation for function setdiff specifies that it treats NaN values as distinct.
You might find the isequaln function to be useful to determine array equality, which treats NaN values as equal to each other, and returns a logical value.
As another work-around to Are Mjaavatten's answer, to obtain the difference between rows, you can also use the following approach:
a = [3 4 5 NaN NaN]; % Considering two example vectors
b = [3 NaN];
a_temp = a(~isnan(a)); % Removing NaN values using isnan() function
b_temp = b(~isnan(b));
setdiff(a_temp, b_temp) % Using setdiff to obtain difference
