The Hub has a button at the top for plugins, to Update Everything. It's obvious that this means "for all sites" - it's a high-level button. There's also a Update Everything button for each site that's opened. But that button also offers to update "all sites". We need to disable all of the sites that we don't want to update.
That's non-intuitive. I expect that behaviour when we're clicking the high-level button. But when we have a single site open and say Update Everything, there's no doubt (in my mind) that we just want to "update all plugins for this one site".