The sandboxing sometimes breaks applications or requires additional configuration. And I don't like that it's a separate thing I need to maintain, although some package managers pair main package updates etc together.

And as a NixOS user, I prefer to use nix to handle as much of my system as possible, although flatpak at least is useful as a fallback in a pinch. Of course, this is a niche within a niche and mainstream users, particularly those using immutable distros can and do benefit from flatpak.