Same album, two different file paths?

[Mnyb]

Unfortunately, I believe this is correct. Why it is, I have no idea, but I do know that splitting an album across folders can cause library indexing problems like you're seeing.

Can it be a consequence of the album art logic ?

In absence of embedded art , the art that resides in the albums folder such as folder.jpg etc is picked as album art.
Therefore an album is also defined as the collection of files in the same folder ( given correct tags , splits inside a folder is possible with bad tags ).