In my experience, Cubase/Nuendo have an issue with handling files of the same name. If I import a number of tracks from CDs, say track 1 of the CD, which Mac defaults to calling something like Audio-01, if I import 2 or more track 1s from different CDs, Nuendo will sometimes play the ‘wrong’ one while displaying the ‘right’ one.
I avoid it by always renaming the audio files before importing them.