When messages XCOMN0288E System function failed, RC=nn (after a transfer to XCOM on Windows) or XCOMU0288E System function failed, RC=nn (after a Transfer to XCOM on Unix) appear then one of two cases happened:
1. You transferred a file to Windows or Unix and one of the optional commands (Preprocessing - XCOMPRE, Post Processing - XENDCMD, Print Jobs - XLPCMD, User Notification - XNOTIFYCMD, Successful Completion - XPPCMD) did not end successful.
2. You transferred a Batch file to Windows or Unix and that Batchfile does not successful execute.
In both cases the system() function is used to initiate these Batch Jobs. It returns an error which is docuemnted in the RC at the end of the message.
So the transfer itself went well but the execution caused a problem. In such cases you need to debug the Batch file as the error is outside of XCOM.