If there are dependent objects between schemas, they'll be pulled in for the comparison, because if you choose to sync the objects without their dependencies the database could be left in an invalid state.
e.g. if you have an object with a dependency on a table in a schema you haven't chosen to compare, that table will show up in the comparison results (and the sync script, if you choose to sync dependencies).
I think that's what's happening here - can you let us know if that's the case?
Do you think this is useful behaviour? What would your expectations be in this situation?