Hi Rohit,
The report will show you all those company codes which are maintained in the same AA which has the report's infoprovider (infocube/multiprovider).
this is under assumption that, in your BI security design you maintain infoprovider attribute and company code attribute in the same AA.
If a user is only able to see some CCodes in the report, that may be because the AA which contains the infocube of this report has less number of CCodes maintained in its infoobject Comp_code.
Thanks, Anish