Standalone Application giving warnings on exit()

I have a top-level .m function that calls a large number of functions and classes compiled into a standalone application, using compiler version: 6.1 (R2015b). The application runs properly, but in order to integrate it with other software, I need to provide an output code to the command interpreter: the same value that would normally be the output of the uncompiled function:

function exitcode = sequence()

From what I understand, the only way of doing this is by using the exit(x) command.

When I call the exit command (line 278-280):

if isdeployed
    exit(exitcode)
end

I get the following warning:

'''

Warning: The file 'C:\Users\xxxx\AppData\Local\Temp\xxxx\mcrCache9.0\TestSoftware\sequence.m' could not be cleared because it contains MATLAB code that is currently executing.

> In sequence.m (line 279)

'''

Every answer I found regarding this warning is "don't use clear all", but I'm not, it seems to be integrated into the exit() command. What can I do to figure out what's producing the warning, and to stop the "MATLAB code that is currently executing"?

Tried the same code on Matlab 2014b, and the warnings don't pop up.