You can get that error if you have an object with the same name as the schema. For example:
create sequence s2;
begin
s2.a;
end;
/
ORA-06550: line 2, column 6:
PLS-00302: component 'A' must be declared
ORA-06550: line 2, column 3:
PL/SQL: Statement ignored
When you refer to S2.MY_FUNC2 the object name is being resolved so it doesn't try to evaluate S2 as a schema name. When you just call it as MY_FUNC2 there is no confusion, so it works.
The documentation explains name resolution. The first piece of the qualified object name - S2 here - is evaluated as an object on the current schema before it is evaluated as a different schema.
It might not be a sequence; other objects can cause the same error. You can check for the existence of objects with the same name by querying the data dictionary.
select owner, object_type, object_name
from all_objects
where object_name = 'S2';