Multitrack sessions normally have more tracks as compared to stem sessions. While stem sessions might only have between four and twenty tracks, multitrack sessions can have tracks from twenty to several hundreds.
Multitrack sessions are often made and expanded during the recording, editing and mixing process. On the other hand, stem sessions are mostly done after the recording, editing and mixing part. However, this is not a fixed rule and there are exceptions.
In certain applications, stems offer more benefits than multitracks.
Stems provide more efficiency for overdubbing. Establishing an overdubbing session in stem will be 10 times faster than doing it in multitrack. The number of files created will also be less, so you can manage them easily.
Mixing stem files is also easier than mixing multitracks. However, there are certain limitations which should be considered. The stem file might already be affected with equalization and reverb from the previous session.
You need to decide on the advantages and disadvantages of stems before you enter into creating them or using them in an audio file.