I found the problem. Before I didn't need to choose restrict to current search (probably always was chosen).
After finally finding all dupes I decided to fix them and only accidentally saw that I planned to delete different books. They have the same author and title. Apparently it is the same book divided to 3 parts. They even have the same ISBN. I was wondering if it is possible for plug in to check series field (it can show if it is different books).
I was wondering the same about formats. Could it search for duplicates with different formats (the ones I would like to merge)? Since know you need to check formats manually.
Also maybe it could search more by size? Calibre shows only 0,X MB. If it showed it more detail in KB it would be easier to see if it is a dupe format.
Just throwing ideas, maybe some can be explored and implemented