Any tips ?

Probably some custom search index files are messed up. Re-indexing could help, only if I could tell you how. I can not point out the problem but If you instead used the Solr Search plugin, the issue is likely to go away...

Thanks İşöğüçı, but reindexing the db does not help. Solr neither. It occurs both with and without Solr

When you say pages do you mean 'pages' from the bundled plugin?
Or is it all types of entities?
I don't know offhand what it might be but a more refined description of the problem may trigger an idea or something.

Matt Gerard problem is .. He uploaded only one file but in search result it shows multiple entity don't know why ..

Even i feel some custom search index files are being indexed twiced.

Proper indexing should solve the issue

@FishKin - there is no indexing by default, search works by direct database query

Is it possible you're using any modified queries that remove the unique modifier for performance or something?

@Matt, there are no modified queries as far as I am aware, but pretty sure of that as well.

@matt, you say that the default search works by direct queries. Would that mean that files have multipe (different) entities with the same metadata ?

How can I identify such items ?

How can I identify such items ?

Look at the guids - if they have different guids then they are different entities with the same data.  If they are the the same guids then your search is in fact returning the same entity multiple times.