I wonder if it has anything to do with deferred segment creation. I'm just guessing here, but if the lob doesn't really exist because of the deferred segments, would the index be created on them?
My other guess is that these may be cross schema indexes. If you exported just scott's objects, then if scott had indexes on a table in another schema, I would think that those would not be exported (depending on the export mode). Can you run dbms_metadata.get_ddl on those indexes to see what the create statement would be? Something like:
SET PAGESIZE 10000
SET LONG 90000000
select dbms_metadata.get_ddl('INDEX', '<NAME>', '<SCHEMA>') FROM SYS.DUAL;
How many rows are in the EMP table ? If the table contains rows, then the deferred segment theory likely will not account for this behavior. I am at a loss to explain the missing indexes. You might want to open an SR on this.
Does the application function normally on the target after the import ?