Registration Form (profile) with selected groups only?
Visibility: Public Pages will be listed; Check your group Admin screen at:

civicrm/group?reset=1


If you're also seeing Groups in your Profile select that are listed as Visibility: User and User Admin Only - do let us know. 

Added: if you don't want all your Groups that are configured Public Pages to be listed then try this:


create a custom field 
add the custom field to the profile
create a smart group - that has your custom field in the search criteria