Exploring what you mean by "placed one photo in two files":
If you managed to import the same image twice (evading the duplicate check on import), the later scan can place them in Duplicates and one can be eliminated.
If those two copies of the same image had been placed into different Albums, Photos will make sure the surviving image is in both Albums at the end of the merge.
If you meant that you assigned one image to two Albums, Duplicates won't see that as a duplicate at all. All of the images in Albums are just pointers to the actual images, which are stored in the library.
When Duplicates is dealing with images of different sizes, qualities, and similar settings, it tries to do the "right thing" which may or may not be your idea of right. That's why you get the opportunity to review the sets of duplicates (triplicates, quadruplicates, etc.) before approving the merge. You might decline the automatic merge and handle it manually or just disallow it if the images are not truly duplicates.