Unfortunately MATLAB does not support stdout or stderr. The closest it has is writing to file 1 (sort of like stdout) or file 2 (sort of like stderr). Both file 1 and file 2 will go to wherever the command output is going, such as the command window. Neither of them are connected to the Unix stderr stream. If the session was started with -nodisplay (or equivalent) so that there is no command window, then both of them are connected to stdout -- but if the command window is active, then neither of them are connected to stdout.
The only difference I have been able to infer in MATLAB between writing to file 1 and file 2, is that it appears from one of the documentation examples (somewhere) that file 2 might not be buffered, that output to it might potentially get mixed in with output that is already in progress.