Because i and j are both functions denoting the imaginary unit:
- http://www.mathworks.co.uk/help/matlab/ref/i.html
- http://www.mathworks.co.uk/help/matlab/ref/j.html
So a variable called i or j will override them, potentially silently breaking code that does complex maths.
Possible solutions include using ii and jj as loop variables instead, or using 1i whenever i is required to represent the imaginary unit.