When your XCOM-Filetransfer ends with message
XCOMN0288E System function failed, RC=nn
XCOMU0288E System function failed, RC=nn
the answer to this question is two-fold.
First, the transfer itself was successful.
Second, this was either a TYPE=JOB transfer or a Transfer with Pre- or Post-Processing. In both cases the execution of the Batch file after the transfer failed for reasons outside XCOM's responsibility. In such cases you need to debug the responsible Batch file.