Hi Jackie, any custom fields that you want in Marketo should really be created in SFDC and then allowed to sync over. If it's visible to the Marketo sync from SFDC, it will be created in Marketo regardless of whether it's a duplicate.
Marketo support can do some custom mapping for you to resolve this, but make sure that you save all of your data in these fields first! I've had one or two custom mappings done, and it deleted all of the data that was in the custom Marketo field.