Are you uploading assets with cost center through LSMW or you are just uploading cost center?
If you are doing the Asset upload with cost center, then check the AO22 - Field status setting of Cost center. If the Maint. Level is ticked for both Main Asset and Sub-Asset and the "Copy" option is checked agaist to it, then the Cost center will be copied from Main asset.
Check it once.
If that is just a cost center master upload, then please check file you are uploaing if there are any spaces, data in next lines......etc