First make very sure they are not in your library.
(perhaps they are not grouped together with the other album songs for some other reason)
Look at the duration of the missing songs, set the panel view to track details, sort by track duration, and see if the tracks are not at the expected position.
Then, maybe the files are corrupt in some way?
(do they play at all when right-clicking 'play with musicbee'?)
To test if corruption might be an issue here, you could encode them to another format, and then try to re-import and see what happens.
(e.g. if they are flac, encode to mp3, if they are mp3, encode to flac)
Not as some definitive solution, but as a means to pinpoint the source of the problem.