Disk IO is what shatters the VM illusion for me right now
I use VMs on my office workstation as a far more convenient substitute for real hardware. In theory I could assemble a physical test machine or a group of them, hook them all up, install things on them, and so on; in practice I virtualize all of that. This means that what I want is the illusion of separate machines and for the most part that's what I get.
However, there's one area where the illusion breaks down and exposes that all of these machines are really just programs on my workstation, and that's disk IO. Because everything is on spinning rust right now (and worse, most of it is on a common set of spinning rust), disk IO in a VM has a clear and visible impact on me trying to do things on my workstation (and vice versa but I generally don't care as much about that). Unfortunately doing things like (re)installing operating systems and performing package updates do a lot of disk IO, often random disk IO.
(In practice neither RAM nor CPU usage break the illusion, partly because I have a lot of both in practice and VMs don't claim all that much of either. It also helps that the RAM is essentially precommitted the moment I start a VM.)
The practical effect is that I generally have to restrict myself to one disk IO intensive thing at once, regardless of where it's happening. This is not exactly a fatal problem, but it is both irritating and a definite crack in the otherwise pretty good illusion that those VMs are separate machines.
(The illusion is increased because I don't interact with them with their nominal 'hardware' console, I do basically everything by ssh'ing in to them. This always seems a little bit Ouroboros-recursive, especially since they have an independent network presence.)