Not sure if this is related, but I tried to move files with identical filenames in the same folder (not albums !) and it would not work. Mind - these identical filenames are actually different files, with different content and metadata. (the filenames are the same because the source are different cameras or a camera's file name counter was reset at some time).
I have not solution so far as to keep them in different folders.
I find it hard to understand that the Photos app seem to rely on filename only to identify unique files, with all that typical image metadata present...