It’s a bug because it’s a new key introduced that doesn’t respect custom keys and it breaks the routines of all developers who have customized F9.
Custom keys should have priority.
Maybe this should be more generically worded in that case (not specific to F9), e.g. “Roblox updates can override custom keyboard shortcuts” or so
It might be more appropriate to file this as a feature request since this is likely something they would need to implement (e.g. prompt you to resolve conflicts in keybinds or notify you about it).
It sounds more like this keybind was implemented without going through the normal pipeline. If not, something odd is definitely going on, because I just checked it out and F9 definitely toggles a breakpoint in the script editor, but the custom shortcut keys window does not show it bound anywhere.
The Cleanup action is not a plugin keybind anyway, but even if it was, this still shouldn’t be happening - there’s a system in place for creating actions via plugins that can be bound to keyboard shortcuts.
I don’t know what happens if Roblox releases a new default keybind that collides with something you have set, but I’m willing to bet it doesn’t overwrite your setting.