Well, things like the fact that snap is supposed to be a distro-agnostic packaging method despite being only truly supported on Ubuntu is annoying. The fact that its locked to the Canonical store is annoying. The fact that it requires a system daemon to function is annoying.
My main gripes with it stem from my job though, since at the university where I work snap has been an absolute travesty;
It overflows the mount table on multi-user systems.
It slows down startup a ridiculous amount even if barely any snaps are installed.
It can’t run user applications if your home drive is mounted over NFS with safe mount options.
It has no way to disable automatic updates during change critical times - like exams.
There’s plenty more issues we’ve had with it, but those are the main ones that keep causing us issues.
Notably Flatpak doesn’t have any of the listed issues, and it also supports both shared installations as well as internal repos, where we can put licensed or bulky software for courses - something which snap can’t support due to the centralized store design.