Sometimes multi-tenancy is a simpler solution because no instance fleet management code needs to be written. With everything there are downsides to multi-tenancy too so you have to weigh the pros and cons for the specific project.
Sometimes this is a feature. If you're doing managed enterprise SaaS then you frequently need to have different customers running on different releases for whatever reason (maybe one customer has a difficult data migration that has to take place before you can upgrade, maybe another customer has something custom that needs to be upgraded in sync).
At the same point if I were hosting something for a group of parties (at my own expense/will/etc.) and I want everyone to just be at version X.Y.Z - having to upgrade each deployment itself is definitely a pain.
Not all software needs to be multi-tenant but it also isn't something that is no longer needed or without thought.