Hi Raja,
If you remove X company code from wrong controlling area assignment ,that co code >> controlling area field must be blank. But if you assigned same company code to other controlling area ,which same controlling area have assignment of multiple company codes,that co code > controlling area field must be as 2. Please controlling area setttings.
Check mentioned SAP note
139905 - Controlling area: T001-KOKFI <> TKA01-KOKFI
Regards
Mani Kumar