Couple of observations:
1. If I delete SOLR data files, repository is reindexed and then search starts to work properly and the same query returns 2 results which is correct.
2. I would say that the duplicate results are caused by moving documents from folder to folder (it finds them in the both old and new folder) and incorrect results are because properties were updated and old value matches the search. I guess SOLR index was not updated correctly when dokument is moved or its property was updated. I tried to reproduce but I couldn't, it looks like it works ok now (after reindex), but I am worried it will come back.