Some Matlab code passed to the server could cause it to hang indefinitely. For example, calling a keyboard statement. Also, it is common practice to have a
dbstop if error
in one's startup.m file. This has the same effect as %pdb in iPython: when an error is encountered, the Matlab interpreter waits for user input. This would be bad in the 'headless' environment of the web server.
At the very least we should have a
dbclear all in webserver.m
We should also try to overload keyboard.m
I have done this before, and it works, but it may depend on the order in which paths are added.

There may be other lurking such gotchas, but these are the principal ones, I think.