Do the duplicates tracks show up with one having the expected file path, and the other with an empty path (viewed in a list with column filename (path))?
If so, you can create a smartlist with the rules:
Filename (path) is <empty>
Media Type is Audio;Image
Apply the rules, select all hits with <Ctrl>+a, and delete.
I occasionally run into this problem, but do not know the root cause. In fact, I ran the smartlist today (after reading your post) and found a large number of "pathless" duplicates for album art - so I just deleted them. In my case, many of these "pathless" duplicates were associated with old albums originally imported long ago. They did not show up in the smartlist when I ran it in the past.
If you find the duplicates all have the same two distinct high level paths, then that should give you a clue about what is going on. You may be able to use a similar smartlist approach, based on path, to delete the undesired duplicates from the library en masse.
Of course, be careful with this stuff and confirm actions with one or a few backed-up hits before any mass deletion.
Win11 Pro (64-bit) | MC 32.0.56 (beta)